from:"lina"

Re: [gmx-users] openmm 3.0, opencl support

2011-04-25 Thread lina

Have you installed the

CUDA Toolkit 4.0 ?
I have never tried, just guessed.

lina

On Mon, Apr 25, 2011 at 9:17 AM, Claus Valka  wrote:

> Hello,
>
> I'm interested in knowing the level of development about gromacs supporting
> the opencl framework language.
>
> I have read the manual about gromacs 4.5.4 that says that opencl is going
> to be supported in future versions. Yet, in the openmm website,
> the new version of openmm (3.0 that is) is supposed to support both cuda
> and opencl framework alongside gromacs:
> (https://simtk.org/project/xml/downloads.xml?group_id=161)
> "The current release of OpenMM and OpenMM-accelerated GROMACS enables
> acceleration of molecular dynamics on specific NVIDIA and ATI GPU cards. "
>
> I downloaded gromacs 4.5.4, along with the openmm 3.0. The installation of
> the packages went fine, yet while trying to build the
> mdrun-gpu option giving the command:
>
> cmake -DGMX_OPENMM=ON
>
> the installation aborted with the error:
>
> CMake Error at cmake/FindCUDA.cmake:465 (message):
>   Specify CUDA_TOOLKIT_ROOT_DIR
> Call Stack (most recent call first):
>   CMakeLists.txt:434 (find_package)
>
>
> -- Configuring incomplete, errors occurred!
>
> Since gromacs developers are working alongside openmm ones:
>
> 1) does gromacs support the opencl framework?
> 2) if the answer to the above is affirmative, what am I supposed to do, so
> as the compilation to succeed?
> 3) if the answer to the 1st question is negative, could you please be more
> specific about the context "future"?
>
> Thank you in advance,
> Nikos
>
>
>
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Re: [gmx-users] amber force field

2011-05-01 Thread lina

In latest version of gromacs (4.5.4 or earlier)

The amber force fields were provided.


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Re: [gmx-users] running job parallel

2011-05-03 Thread lina

Hi,

I don't know the specific cluster you mentioned.

but when I met such problems, I used to check the .log which usually
gave me very helpful information.
and I used to use some script to submit job,

I post one as example, please set the proper one according to your cluster.

more openmpi_parallel.sh
#!/bin/bash
#PBS -N jobname
#PBS -j oe
#PBS -V

#PBS -l nodes=2:ppn=8

## pre-processing script
cd $PBS_O_WORKDIR
NCPUS=`cat $PBS_NODEFILE | wc -l`
echo $NCPUS

# ###
# PATH for Intel Compiler and OpenMPI
# 
export PATH=/opt/intel/composerxe-2011.2.137/bin/intel64:/usr/local/mpi/intel/bi
n:/usr/local/fftw/bin:/usr/local/gromacs/bin:i${PATH}

export LD_LIBRARY_PATH=/usr/local/fftw/lib:/opt/intel/composerxe-2011.2.137/mkl/
lib/intel64:/opt/intel/lib/intel64:/usr/local/mpi/intel/lib:${LD_LIBRARY_PATH}

# 
# commands to launch OpenMPI jobs
# 
/usr/local/mpi/intel/bin/mpirun -np $NCPUS -machinefile $PBS_NODEFILE $PBS_O_WOR
KDIR/$file


# #
# PATH for GNU Compiler and OpenMPI
# ##
# export PATH=/usr/local/mpi/gnu/bin:/usr/local/fftw/bin:/usr/local/gromacs/bin:
${PATH}
# export LD_LIBRARY_PATH=/usr/local/fftw/lib:/usr/lib64:${LD_LIBRARY_PATH}

# ##
# Using GNU Compiler and OpenMPI
# ##
# /usr/local/mpi/gnu/bin/mpirun -np $NCPUS -machinefile $PBS_NODEFILE $PBS_O_WOR
KDIR/$file

# #
# Optional LD_LIBRARY_PATH if not using MKL
# #
# export LD_LIBRARY_PATH=/usr/local/atlas/lib:${LD_LIBRARY_PATH}
# export LD_LIBRARY_PATH=/usr/local/blacs/lib:${LD_LIBRARY_PATH}
# export LD_LIBRARY_PATH=/usr/local/lapack/lib:${LD_LIBRARY_PATH}
# export LD_LIBRARY_PATH=/usr/local/salapack/lib:${LD_LIBRARY_PATH}


You are welcome,


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[gmx-users] about g_hbond

2011-05-11 Thread lina

Hi,

For group A, b, C.

It's no doubt can get hb forming number between A-b, b-C. b-(A or C).

But I don't know how to get the number of residues of b forming both
with A and B at the same time. namely b-A&C, not with AC group.

Thanks,
--
Best Regards,

lina



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Re: [gmx-users] about g_hbond

2011-05-11 Thread lina

On Wed, May 11, 2011 at 11:10 PM, Justin A. Lemkul  wrote:
>
>
> lina wrote:
>>
>> Hi,
>>
>> For group A, b, C.
>>
>> It's no doubt can get hb forming number between A-b, b-C. b-(A or C).
>>
>> But I don't know how to get the number of residues of b forming both
>> with A and B at the same time. namely b-A&C, not with AC group.
>>
>
> There's no direct way to do it, but from the output files of g_hbond it can
> be done.  You'd need the .xpm files of A-C and B-C hydrogen bonds, and write
> some script that parses the .xpm files, and whenever there is an entry of
> A-C in the same frame as B-C, then you have a hydrogen bond mediated between
> the two. There's lots of discussion in the list archive about water-mediated
> hydrogen bonds that is likely applicable here.

Thanks, I will try.

>
> Note that if you're using g_hbond in version 4.5, there is an important bug
> that was fixed just yesterday:
>
> http://lists.gromacs.org/pipermail/gmx-users/2011-May/061249.html

I noticed yesterday and recompiled the gromacs already. Thanks for reminding.

>
> -Justin
>
>> Thanks,
>> --
>> Best Regards,
>>
>> lina
>>
>>
>>
>
> --
> 
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> 
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lina
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Re: [gmx-users] about g_hbond

2011-05-11 Thread lina

/* y-label: "Hydrogen Bond Index" */

is it relevant to the total number of hydrogen bonds?

such as
/* XPM */
/* x-label: "Time (ps)" */
/* y-label: "Hydrogen Bond Index" */
/* type:"Discrete" */
static char *gromacs_xpm[] = {

A-b : "51 84   2 1",

b-C : "51 95   2 1",

84, 95?

Thanks,
On Wed, May 11, 2011 at 11:10 PM, Justin A. Lemkul  wrote:
>
>
> lina wrote:
>>
>> Hi,
>>
>> For group A, b, C.
>>
>> It's no doubt can get hb forming number between A-b, b-C. b-(A or C).
>>
>> But I don't know how to get the number of residues of b forming both
>> with A and B at the same time. namely b-A&C, not with AC group.
>>
>
> There's no direct way to do it, but from the output files of g_hbond it can
> be done.  You'd need the .xpm files of A-C and B-C hydrogen bonds, and write
> some script that parses the .xpm files, and whenever there is an entry of
> A-C in the same frame as B-C, then you have a hydrogen bond mediated between
> the two.

> There's lots of discussion in the list archive about water-mediated
> hydrogen bonds that is likely applicable here.
>
> Note that if you're using g_hbond in version 4.5, there is an important bug
> that was fixed just yesterday:
>
> http://lists.gromacs.org/pipermail/gmx-users/2011-May/061249.html
>
> -Justin
>
>> Thanks,
>> --
>> Best Regards,
>>
>> lina
>>
>>
>>
>
> --
> 
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> 
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lina
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Re: [gmx-users] about g_hbond

2011-05-12 Thread lina

I got it.  I should have outputted the -hbn file.


Thanks,

On Thu, May 12, 2011 at 1:09 PM, lina  wrote:
> /* y-label: "Hydrogen Bond Index" */
>
> is it relevant to the total number of hydrogen bonds?
>
> such as
> /* XPM */
> /* x-label: "Time (ps)" */
> /* y-label: "Hydrogen Bond Index" */
> /* type:    "Discrete" */
> static char *gromacs_xpm[] = {
>
> A-b : "51 84   2 1",
>
> b-C : "51 95   2 1",
>
> 84, 95?
>
> Thanks,
> On Wed, May 11, 2011 at 11:10 PM, Justin A. Lemkul  wrote:
>>
>>
>> lina wrote:
>>>
>>> Hi,
>>>
>>> For group A, b, C.
>>>
>>> It's no doubt can get hb forming number between A-b, b-C. b-(A or C).
>>>
>>> But I don't know how to get the number of residues of b forming both
>>> with A and B at the same time. namely b-A&C, not with AC group.
>>>
>>
>> There's no direct way to do it, but from the output files of g_hbond it can
>> be done.  You'd need the .xpm files of A-C and B-C hydrogen bonds, and write
>> some script that parses the .xpm files, and whenever there is an entry of
>> A-C in the same frame as B-C, then you have a hydrogen bond mediated between
>> the two.
>
>> There's lots of discussion in the list archive about water-mediated
>> hydrogen bonds that is likely applicable here.
>>
>> Note that if you're using g_hbond in version 4.5, there is an important bug
>> that was fixed just yesterday:
>>
>> http://lists.gromacs.org/pipermail/gmx-users/2011-May/061249.html
>>
>> -Justin
>>
>>> Thanks,
>>> --
>>> Best Regards,
>>>
>>> lina
>>>
>>>
>>>
>>
>> --
>> 
>>
>> Justin A. Lemkul
>> Ph.D. Candidate
>> ICTAS Doctoral Scholar
>> MILES-IGERT Trainee
>> Department of Biochemistry
>> Virginia Tech
>> Blacksburg, VA
>> jalemkul[at]vt.edu | (540) 231-9080
>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>
>> 
>> --
>> gmx-users mailing list    gmx-users@gromacs.org
>> http://lists.gromacs.org/mailman/listinfo/gmx-users
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>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
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>>
>
>
>
> --
> Best Regards,
>
> lina
>



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lina
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Re: [gmx-users] index file

2011-05-12 Thread lina

make_ndx -f your.gro/pdb -n your.ndx -o your.ndx

LiGA & LİGB:
q

in grompp add -n your.ndx


2011/5/12 ahmet yıldırım :
> Dear users,
>
> I have two ligands. I created a special index group that merges the protein,
> LiGA and LİGB.
>
> I have the pr.mdp file as the following:
> ...
> energygrps  = Protein    LİGA_LİGB
> tc-grps = Protein_LİGA_LİGB    Water_and_ions
> ...
>
> grompp -f pr.mdp -p topol.top -c em.gro -n index.ndx -o pr.tpr
> Fatal error:
> Group LİGA_LİGB not found in indexfile.
>
> I get the fatal error since I dont have a special index group that merges
> LiGA and LİGB. should I create two different index file?
>
> Thanks in advance
> --
> Ahmet YILDIRIM
>
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lina
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Re: [gmx-users] index file

2011-05-12 Thread lina

2011/5/12 Justin A. Lemkul :
>
>
> lina wrote:
>>
>> make_ndx -f your.gro/pdb -n your.ndx -o your.ndx
>>
>> LiGA & LİGB:
>
> This is not correct.  You need to use | rather than &.  Using logical and
> (&) means the index group will contain atoms that are common to both LIGA
> and LIGB.  If they are distinct entities, the group will be empty.  Logical
> or (|) says merge the two different groups to create one unified group.

Ooops


>
> -Justin
>
>> q
>>
>> in grompp add -n your.ndx
>>
>>
>> 2011/5/12 ahmet yıldırım :
>>>
>>> Dear users,
>>>
>>> I have two ligands. I created a special index group that merges the
>>> protein,
>>> LiGA and LİGB.
>>>
>>> I have the pr.mdp file as the following:
>>> ...
>>> energygrps      = Protein    LİGA_LİGB
>>> tc-grps         = Protein_LİGA_LİGB    Water_and_ions
>>> ...
>>>
>>> grompp -f pr.mdp -p topol.top -c em.gro -n index.ndx -o pr.tpr
>>> Fatal error:
>>> Group LİGA_LİGB not found in indexfile.
>>>
>>> I get the fatal error since I dont have a special index group that merges
>>> LiGA and LİGB. should I create two different index file?
>>>
>>> Thanks in advance
>>> --
>>> Ahmet YILDIRIM
>>>
>>> --
>>> gmx-users mailing list    gmx-users@gromacs.org
>>> http://lists.gromacs.org/mailman/listinfo/gmx-users
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>>>
>>
>>
>>
>
> --
> 
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> 
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lina
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Re: [gmx-users] hi

2011-05-29 Thread lina

On May 29, 2011, at 20:45, rashi.pari...@gmail.com wrote:

> Hi all..
> I want to ask if it is possible to restart the md run if due to power problem 
> final md run not completed means initiating md from where is stop due to any 
> reason?

Suppose your .tpr is topol.tpr

mdrun -cpi state.cpt 

Or suppose your .tpr is my.tpr

You may try

mdrun -deffnm my -cpi my.cpt 

As suggested by others. Start learning read mdrun --h

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Re: [gmx-users] binaries for mac os x 10.6

2011-06-04 Thread lina

On Sun, Jun 5, 2011 at 6:12 AM,   wrote:
> Dear Users:
>
> Does somebody have a set of gromacs binaries for mac os X 10.6.7 that they
> can post somewhere (perhaps in
> http://www.gromacs.org/Downloads/User_contributions/Gromacs_binaries)?
>
> Macbook Air 3.1
> Version 10.6.7
> 1.4 GHz Intel Core 2 Duo
> 2 GB 1067 MHz DDR3
> SMC version 1.67f3
>
>
> I am trying to install it on a macbook air and I can't imagine using up 4 GB
> of the 64 GB hard drive to install xcode and do an install from source. Even
> tools like fink seem to require xcode.

The .dmg is more than 4GB, but after installation it won't swallow 4GB.

>
> I'm very new to the mac (it's not even my mac) so if anybody has better
> ideas for getting a gromacs installation then that would be great.
>
> Please note that I did try to search the archives, but for some reason a
> search for the word "gromacs" turned up many hits but a search for "mac" or
> "max os X 10.6" or variation therein turned up no hits... possibly because
> the words are so short? A google serch turned up a bit, but not what I am
> looking for.
>
> Thank you very much for your time,
> Chris.
>
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Re: [gmx-users] g_hbond/g_sas - how is it calculated?

2011-06-08 Thread lina

On Wed, Jun 8, 2011 at 10:20 PM, Marzinek, Jan
 wrote:
> Hi,
>
>
>
> I have a question related to the calculation of hydrogen bonds in Gromacs.
> As I read in Manual it comes from the distance between donor and acceptor (
> <= 0.35 nm) and the angle <=30 degr beween hydrogen and acceptor. The
> question is - why 30 degr? How is it related to the reality?

It's a default value, you can change it when you need.

>
>
>
> The second thing is the claculation of the accessible surface area
> (g_sas) of the molecule for instance? It is not explained in manual and I am
> really curious how g_sas makes these calculations.
>
> As my supervisors do not know the gromacs their questions are always about
> such details :)
>
> However, I think it is really important to understand what you are really
> doing using commands in Gromacs which provide you with really detailed
> results.

All I can say is that, practice and problems are a good teacher.

>
>
>
> Thank you in advance,
>
>
>
> Jan
>
>
> --
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-- 
Best Regards,

lina
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Re: [gmx-users] unscribe

2012-01-11 Thread lina

On Thursday 12,January,2012 09:36 AM, yp sun wrote:

Dear Sir,
I want to unscribe there emails, thank.

http://lists.gromacs.org/mailman/listinfo/gmx-users

at the bottom, fill in your email address and click Unsubscribe.

Yeping Sun
CAS Key Laboratory of Pathogenic Microbiology & Immunology
INSTITUTE OF MICROBIOLOGY CHINESE ACADEMY OF SCIENCES
NO.1 Beichen West Road,Chaoyang District,Beijing 100101,china

--- *12年1月12日，周四, Mark Abraham //* 写道：

发件人: Mark Abraham 
主题: Re: [gmx-users] REMD error
收件人: "Discussion list for GROMACS users" 
日期: 2012年1月12日,周四,上午9:28

On 12/01/2012 11:54 AM, bharat gupta wrote:
 > Hi,
 >
 > I am trying to run a REMD of a peptide. But while executing the
following command after nvt and npt equilibration , I am getting the
following error:-
 >
 > mdrun_mpi mdrun -s prefix_.tpr -multi 20 -replex 1000
 > mdrun_mpi: error while loading shared libraries: libgmx_mpi.so.6:
cannot enable executable stack as shared object requires: Permission
denied
 >

You configured GROMACS to use shared libraries, but something about
them or your current environment doesn't work. Try rebuilding
GROMACS, building with static libraries, or discussing with your
system admins.

Mark
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Re: [gmx-users] REMD error

2012-01-11 Thread lina


On Thursday 12,January,2012 08:54 AM, bharat gupta wrote:

Hi,

I am trying to run a REMD of a peptide. But while executing the
following command after nvt and npt equilibration , I am getting the
following error:-

mdrun_mpi mdrun -s prefix_.tpr -multi 20 -replex 1000
mdrun_mpi: error while loading shared libraries: libgmx_mpi.so.6: cannot
enable executable stack as shared object requires: Permission denied


Can you run a normal md smoothly?
try:
mdrun_mpi mdrun -deffnm prefix_0

if it works, then some of your trajectories not sound. means system does 
not equilibrium well.



Can anybody suggest me how could I rectify this error.

--
Bharat



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[gmx-users] Failed to lock: md.log. No locks available.

2012-01-13 Thread lina

Hi,

Failed to lock: md.log. No locks available.

still the same problem I met before,

once I terminated, resume not work, there is a md.log file.

$ mount
/dev/sda1 on / type ext3 (rw)
none on /proc type proc (rw)
none on /sys type sysfs (rw)
none on /dev/pts type devpts (rw,gid=5,mode=620)
usbfs on /proc/bus/usb type usbfs (rw)
none on /dev/shm type tmpfs (rw)
none on /proc/sys/fs/binfmt_misc type binfmt_misc (rw)
sunrpc on /var/lib/nfs/rpc_pipefs type rpc_pipefs (rw)
honeydewlocal:/vol/hpc_vol/HomeHPC on /home type nfs
(rw,rsize=32k,wsize=32k,intr,hard,tcp,addr=192.168.5.83)

The /home is mounting on the last one.

CPU: 8 Intel(R) Xeon(R) Dual-Core 3.33 Ghz
Memory: 114GB RAM
HDD Size: 744GB
OS: CentOS 4 (64-bits)

Thanks for any suggestions,

any additional info you need please let me know,

Best regards,
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Re: [gmx-users] Failed to lock: md.log. No locks available.

2012-01-13 Thread lina

On Fri, Jan 13, 2012 at 4:57 PM, Mark Abraham  wrote:
> On 13/01/2012 7:08 PM, lina wrote:
>>
>> Hi,
>>
>> Failed to lock: md.log. No locks available.
>
>
> mdrun locks various files at various points. If it can't then GROMACS won't
> continue, but the problem lies with the file system, and not with GROMACS.
> Possibly some phantom process still thinks it owns the file.

It's something relevant to the server.
I am not experienced to figure it out even did some rough try.
will drop an email to administrator.

Thanks,

>
> Mark
>
>
>>
>> still the same problem I met before,
>>
>> once I terminated, resume not work, there is a md.log file.
>>
>> $ mount
>> /dev/sda1 on / type ext3 (rw)
>> none on /proc type proc (rw)
>> none on /sys type sysfs (rw)
>> none on /dev/pts type devpts (rw,gid=5,mode=620)
>> usbfs on /proc/bus/usb type usbfs (rw)
>> none on /dev/shm type tmpfs (rw)
>> none on /proc/sys/fs/binfmt_misc type binfmt_misc (rw)
>> sunrpc on /var/lib/nfs/rpc_pipefs type rpc_pipefs (rw)
>> honeydewlocal:/vol/hpc_vol/HomeHPC on /home type nfs
>> (rw,rsize=32k,wsize=32k,intr,hard,tcp,addr=192.168.5.83)
>>
>> The /home is mounting on the last one.
>>
>> CPU: 8 Intel(R) Xeon(R) Dual-Core 3.33 Ghz
>> Memory: 114GB RAM
>> HDD Size: 744GB
>> OS: CentOS 4 (64-bits)
>>
>> Thanks for any suggestions,
>>
>> any additional info you need please let me know,
>>
>> Best regards,
>
>
> --
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Re: [gmx-users] Failed to lock: md.log. No locks available.

2012-01-13 Thread lina

On Fri, Jan 13, 2012 at 7:04 PM, Jianguo Li  wrote:
> There is a solution in this mailing list sometime before:
> mv md.log to some other folder and copy it back.
> Jianguo

I tried, not work.

Thanks,

> ____
> From: lina 
> To: Discussion list for GROMACS users 
> Sent: Friday, 13 January 2012, 18:51
> Subject: Re: [gmx-users] Failed to lock: md.log. No locks available.
>
> On Fri, Jan 13, 2012 at 4:57 PM, Mark Abraham 
> wrote:
>> On 13/01/2012 7:08 PM, lina wrote:
>>>
>>> Hi,
>>>
>>> Failed to lock: md.log. No locks available.
>>
>>
>> mdrun locks various files at various points. If it can't then GROMACS
>> won't
>> continue, but the problem lies with the file system, and not with GROMACS.
>> Possibly some phantom process still thinks it owns the file.
>
> It's something relevant to the server.
> I am not experienced to figure it out even did some rough try.
> will drop an email to administrator.
>
> Thanks,
>
>>
>> Mark
>>
>>
>>>
>>> still the same problem I met before,
>>>
>>> once I terminated, resume not work, there is a md.log file.
>>>
>>> $ mount
>>> /dev/sda1 on / type ext3 (rw)
>>> none on /proc type proc (rw)
>>> none on /sys type sysfs (rw)
>>> none on /dev/pts type devpts (rw,gid=5,mode=620)
>>> usbfs on /proc/bus/usb type usbfs (rw)
>>> none on /dev/shm type tmpfs (rw)
>>> none on /proc/sys/fs/binfmt_misc type binfmt_misc (rw)
>>> sunrpc on /var/lib/nfs/rpc_pipefs type rpc_pipefs (rw)
>>> honeydewlocal:/vol/hpc_vol/HomeHPC on /home type nfs
>>> (rw,rsize=32k,wsize=32k,intr,hard,tcp,addr=192.168.5.83)
>>>
>>> The /home is mounting on the last one.
>>>
>>> CPU: 8 Intel(R) Xeon(R) Dual-Core 3.33 Ghz
>>> Memory: 114GB RAM
>>> HDD Size: 744GB
>>> OS: CentOS 4 (64-bits)
>>>
>>> Thanks for any suggestions,
>>>
>>> any additional info you need please let me know,
>>>
>>> Best regards,
>>
>>
>> --
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>> http://lists.gromacs.org/mailman/listinfo/gmx-users
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[gmx-users] force field

2012-01-23 Thread lina

Hi,

which gromacs force field shares the high "quasi-compatibility" with
the amber force field.

I checked the heme only exists in gromos and the charmn

while gbsa only shows in amber and oplsaa,

truth is that I don't know how to get the gbsa parameter for heme,

Thanks for any suggestions,

Best regards,
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Re: [gmx-users] Implicit solvent model in Gromacs

2012-01-23 Thread lina

On Mon, Jan 23, 2012 at 10:01 AM, Gianluca Interlandi
 wrote:
> Dear gromacs users list,
>
> I noticed that gromacs can perform simulations with an implicit solvent
> model using a GBSA method. Is it compatible with the CHARMM22 force field?

look for gbsa.itp showed

amber03.ff/forcefield.itp
amber03.ff/gbsa.itp
amber94.ff/forcefield.itp
amber94.ff/gbsa.itp
amber96.ff/forcefield.itp
amber96.ff/gbsa.itp
amber99.ff/forcefield.itp
amber99.ff/gbsa.itp
amber99sb.ff/forcefield.itp
amber99sb.ff/gbsa.itp
amber99sb-ildn.ff/forcefield.itp
amber99sb-ildn.ff/gbsa.itp
amberGS.ff/forcefield.itp
amberGS.ff/gbsa.itp
oplsaa.ff/forcefield.itp
oplsaa.ff/gbsa.itp

seems not.

>
> Thanks,
>
>     Gianluca
>
> -
> Gianluca Interlandi, PhD gianl...@u.washington.edu
>                    +1 (206) 685 4435
>                    http://artemide.bioeng.washington.edu/
>
> Postdoc at the Department of Bioengineering
> at the University of Washington, Seattle WA U.S.A.
> -
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Re: [gmx-users] About g_rms and the XPM file format

2012-01-23 Thread lina

On Mon, Jan 23, 2012 at 9:56 PM, Víctor  wrote:
> Dear all,
>
> I've been trying to do a rmsd matrix of  two different trajectories by using
> g_rms (with -f traj1 and -f2 traj2). I'm wondering if the algorithm g_rms
> uses does something like this:
>
> for each frame f1 in traj1:
>   for each frame f2 in traj2:
>     superimpose f1 , f2
>     calculateRMSD f1, f2
>
> Or like this (as I've seen in some other rmsd matrix calculation scripts):
>
> for each frame f in traj1:
>   superimpose f with first frame
>
> for each frame f1 in traj1:
>   for each frame f2 in traj2:
>     calculateRMSD f1, f2
>
> I've also been trying to convert the resulting xpm file to a readable file

BTW, xpm file is readable.
try:
more xpm or other tools your preferred to read.


> in order to process it using python. Is there any tool to do this kind of
> conversion?(Btw I've been trying to find this kind of tool with not much
> luck). There's enough info on the file to be able to parse it easily, but
> using a 3rd party tested tool would be more convenient.
>
> Thanks!
>
> --
>
> Víctor Gil Sepúlveda
> E. Informatica - FIB - UPC
>
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Re: [gmx-users] Implicit solvent model in Gromacs

2012-01-23 Thread lina

On Tue, Jan 24, 2012 at 12:08 AM, Justin A. Lemkul  wrote:
>
>
> lina wrote:
>>
>> On Mon, Jan 23, 2012 at 10:01 AM, Gianluca Interlandi
>>  wrote:
>>>
>>> Dear gromacs users list,
>>>
>>> I noticed that gromacs can perform simulations with an implicit solvent
>>> model using a GBSA method. Is it compatible with the CHARMM22 force
>>> field?
>>
>>
>> look for gbsa.itp showed
>>
>> amber03.ff/forcefield.itp
>> amber03.ff/gbsa.itp
>> amber94.ff/forcefield.itp
>> amber94.ff/gbsa.itp
>> amber96.ff/forcefield.itp
>> amber96.ff/gbsa.itp
>> amber99.ff/forcefield.itp
>> amber99.ff/gbsa.itp
>> amber99sb.ff/forcefield.itp
>> amber99sb.ff/gbsa.itp
>> amber99sb-ildn.ff/forcefield.itp
>> amber99sb-ildn.ff/gbsa.itp
>> amberGS.ff/forcefield.itp
>> amberGS.ff/gbsa.itp
>> oplsaa.ff/forcefield.itp
>> oplsaa.ff/gbsa.itp
>>
>> seems not.
>>
>
> It's called gb.itp in the charmm27.ff subdirectory.

Thanks. your information is very helpful. I know the answer asked on
another thread.

>
> -Justin
>
>
>>> Thanks,
>>>
>>>    Gianluca
>>>
>>> -
>>> Gianluca Interlandi, PhD gianl...@u.washington.edu
>>>                   +1 (206) 685 4435
>>>                   http://artemide.bioeng.washington.edu/
>>>
>>> Postdoc at the Department of Bioengineering
>>> at the University of Washington, Seattle WA U.S.A.
>>> -
>>> --
>>> gmx-users mailing list    gmx-users@gromacs.org
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>
>
> --
> 
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> 
>
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Re: [gmx-users] Installing & uninstalling of gromacs

2012-01-23 Thread lina

On 24 Jan, 2012, at 1:53, Spring buds  wrote:

> Dear Gromacs users,
> 
> Greetings!!!
> 
> I am very new users and I am trying to install grmacs 4.5.5 or 3.3.3 for past 
> four days. But still I am not able to. So I would like to ask some questions 
> which are below.
> 
> 
> 1.My laptop is a dual core, which means two processors?.So should I need to 
> install MPI?
> 
--enable threads 

> 2.I installed gromacs 4.5.5 with mistakes. To remove installing, I used the 
> "which gromacs" and it shows as "/usr/bin/which: no mdrun in 
> (/usr/kerberos/bin:/usr/local/bin:/usr/bin:/bin:/usr/X11R6/bin:/home/Malai/bin)".
>  However, I used "rm -rf /usr/local/gromacs" to remove installing I still can 
> see tha gromacs files with red background in "/usr/local/bin". Could you tell 
> me I removed the gromacs installing?

You have not.  

> 
> 3.Could you please tell me the very simple steps for installatios, since I am 
> a novice. 

http://www.gromacs.org/Downloads/Installation_Instructions

> 
> Many thanks in advance for your time and help.
> 
> Huang Malai
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Re: [gmx-users] Installing & uninstalling of gromacs

2012-01-23 Thread lina

On Tue, Jan 24, 2012 at 11:42 AM, Spring buds  wrote:
> Hi lina,
>
> Thanks for reply. could you tell me how to remove completly the gromacs
> installation?

Which commands have you issued?

try make uninstall in the directory where you used make install
before. like Path_to//gromacs-4.5.5
and then make distclean
for a totally clear re-installation, removed the /gromac-4.5.5 and
re-untar the gromacs-4.5.5.tar.gz

before that, further check the lib and bin have totally removed or not.

Which OS you are working on?

>
>
> On Tue, Jan 24, 2012 at 2:31 AM, lina  wrote:
>>
>> On 24 Jan, 2012, at 1:53, Spring buds  wrote:
>>
>> > Dear Gromacs users,
>> >
>> > Greetings!!!
>> >
>> > I am very new users and I am trying to install grmacs 4.5.5 or 3.3.3 for
>> > past four days. But still I am not able to. So I would like to ask some
>> > questions which are below.
>> >
>> >
>> > 1.My laptop is a dual core, which means two processors?.So should I need
>> > to install MPI?
>> >
>> --enable threads
>>
>> > 2.I installed gromacs 4.5.5 with mistakes. To remove installing, I used
>> > the "which gromacs" and it shows as "/usr/bin/which: no mdrun in
>> > (/usr/kerberos/bin:/usr/local/bin:/usr/bin:/bin:/usr/X11R6/bin:/home/Malai/bin)".
>> > However, I used "rm -rf /usr/local/gromacs" to remove installing I still 
>> > can
>> > see tha gromacs files with red background in "/usr/local/bin". Could you
>> > tell me I removed the gromacs installing?
>>
>> You have not.
>>
>> >
>> > 3.Could you please tell me the very simple steps for installatios, since
>> > I am a novice.
>>
>> http://www.gromacs.org/Downloads/Installation_Instructions
>>
>> >
>> > Many thanks in advance for your time and help.
>> >
>> > Huang Malai
>> > --
>> > gmx-users mailing list    gmx-users@gromacs.org
>> > http://lists.gromacs.org/mailman/listinfo/gmx-users
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>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
>
>
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[gmx-users] adding hydrogen

2012-01-25 Thread lina

Hi,

are there some tips of quick adding missing atoms ( namely hydrogens,
non-titrable ones, or some ligands ones) ?

Thanks,
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Re: [gmx-users] umbrella-drug

2012-01-28 Thread lina

On Sat, Jan 28, 2012 at 9:17 PM, parto haghighi
 wrote:
> Dear gmx-users
> I am working on lipid membrane+drug system.I should do umbrella
> sampling in this procedure:
> 1.cat drug and lipid
> 2.energy minimization
> 3.run npt
> 4.run md_pull
> I want to pull drug into the membrane but gromacs pushes the drug to
> the sides of box.and this result is independent of drug location
> Also I have used 500 ps for my simulation time but when I use ngmx to
> see the process,it runs only 56 ps.why?
> What can I do when I want to move drug to the bilayer?
You may want to check the
pull_vec1
and
pull_k

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Re: [gmx-users] simulation killed

2012-01-29 Thread lina

On Mon, Jan 30, 2012 at 1:18 AM, murat özçelik  wrote:
> hi again capacity of my harddisk 600 GB ı try again ..the program
> gave me below message...
>
> Reading file md0.tpr, VERSION 4.5.4 (single precision)
> Starting 8 threads
>
> NOTE: The load imbalance in PME FFT and solve is 1211%.
>   For optimal PME load balancing
>   PME grid_x (1152) and grid_y (1152) should be divisible by
> #PME_nodes_x (8)
>   and PME grid_y (1152) and grid_z (1152) should be divisible by
> #PME_nodes_y (1)
>
>
> Making 1D domain decomposition 8 x 1 x 1
> starting mdrun 'Protein in water'

> 250 steps,   5000.0 ps.
> ./job_0.sh: line 95: 15777 Killed  mdrun -nt 8 -deffnm

What's inside your job_0.sh?

something wrong your script.

> md$LAMBDA
>
> Production MD complete.
> Ending. Job completed for lambda = 0
> mkiytak@babil:~/JOB1$
>
>
> How can I solve this problemthanks for your help.
>
>
>
>
>
>
>
>> Date: Sun, 29 Jan 2012 10:43:53 -0600
>> From: p...@uab.edu
>> To: gmx-users@gromacs.org
>> Subject: Re: [gmx-users] simulation killed
>
>>
>> something killed your job but it wasn't gromacs.
>> Your system has run time or memory requirements that your job exceeded.
>>
>> On 2012-01-29 06:40:29PM +0200, mehmet kıytak wrote:
>> > hi! all
>> >
>> > ı have to a big problem..ı am doing free energy calculation for a ligand
>> > (L
>> > histidine ) when ı perform mdrun .. my simulation stop ... the program
>> > gave
>> > me this message..
>> >
>> > Reading file md0.tpr, VERSION 4.5.4 (single precision)
>> > Starting 8 threads
>> > Making 1D domain decomposition 8 x 1 x 1
> & gt; > starting mdrun 'Protein in water'
>
>> > 250 steps, 5000.0 ps.
>> > ./job_0.sh: line 95: 15457 Killed mdrun -nt 8 -deffnm
>> > md$LAMBDA
>> > Production MD complete.
>> > Ending. Job completed for lambda = 0
>> > mkiytak@babil:~/JOB1$
>> >
>> >
>> > my mdp file..
>> >
>> > ; Run control
>> > integrator = sd ; Langevin dynamics
>> > tinit = 0
>> > dt = 0.002
>> > nsteps = 250 ; 5 ns
>> > nstcomm = 100
>> > ; Output control
>> > nstxout = 500
>> > nstvout = 500
>> > nstfout = 0
>> > nstlog = 500
>> > nstenergy = 500
>> > nstxtcout = 0
>> > xtc-precision = 1000
>> > ; Neighborsearching and short-range nonbonded interactions
>> > nstlist = 10
>> > ns_type = grid
>> > pbc = xyz
>> > rlist = 1.0
>> > ; Electrostatics
>> > coulombtype = PME
>> > rcoulomb = 1.0
>> > ; van der Waals
>> > vdw-type = switch
>> > rvdw-switch = 0.8
>> > rvdw = 0.9
>> > ; Apply long range dispersion corrections for Energy and Pressure
>> > DispCorr = EnerPres
>> > ; Spacing for the PME/PPPM FFT grid
>> > fourierspacing = 0.12
>> > ; EWALD/PME/PPPM parameters
>> > pme_order = 6
>> > ewald_rtol = 1e-06
>> > epsilon_surface = 0
>> > optimize_fft = no
>> &g t; ; Temperature coupling
>
>> > ; tcoupl is implicitly handled by the sd integrator
>> > tc_grps = system
>> > tau_t = 1.0
>> > ref_t = 300
>> > ; Pressure coupling is on for NPT
>> > Pcoupl = Parrinello-Rahman
>> > tau_p = 0.5
>> > compressibility = 4.5e-05
>> > ref_p = 1.0
>> > ; Free energy control stuff
>> > free_energy = yes
>> > init_lambda = 0.00
>> > delta_lambda = 0
>> > foreign_lambda = 0.05
>> > sc-alpha = 0.5
>> > sc-power = 1.0
>> > sc-sigma = 0.3
>> > couple-moltype = system
>> > couple-lambda0 = vdw ; only van der Waals interactions
>> > couple-lambda1 = non e ; turn off everything, in this case
>
>> > only vdW
>> > couple-intramol = no
>> > nstdhdl = 10
>> > ; Do not generate velocities
>> > gen_vel = no
>> > ; options for bonds
>> > constraints = h-bonds ; we only have C-H bonds here
>> > ; Type of constraint algorithm
>> > constraint-algorithm = lincs
>> > ; Constrain the starting configuration
>> > ; since we are continuing from NPT
>> > continuation = yes
>> > ; Highest order in the expansion of the constraint coupling matrix
>> > lincs-order = 12
>> >
>> > PLEASE HELP ME... WHY THE PROGRAM STOP ( KİLLED) SORRY FOR BAD ENGLİSH..
>>
>> > --
>> > gmx-users mailing list gmx-users@gromacs.org
>> > http://lists.gromacs.org/mailman/listinfo/gmx-users
>> > Please search the archive at
>> > http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>> > Please don't post (un)subscribe requests to the list. Use the
>> > www interface or send it to gmx-users-requ...@gromacs.org.
>> > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>>
>> --
>> ==
>> Peter C. Lai | University of Alabama-Birmingham
>> Programmer/Analyst | KAUL 752A
>> Genetics, Div. of Research | 705 South 20th Street
>> p...@uab.edu | Birmingham AL 35294-4461
>> (205) 690-0808 |
>> ==
>>
>> --
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Re: [gmx-users] Trajectory

2012-01-30 Thread lina

On Mon, Jan 30, 2012 at 5:43 PM, Steven Neumann  wrote:
> Dear Gmx Users,
>
> I run the simulation of protein with 10 ligands (200 ns). In total I should
> have total of 4000 frames as I set up:
>
> nsteps = 1
>
> dt = 0.002
>
> nstxout = 25000
>
> I used trjconv -f md.trr -o mdnojump.xtc -pbc nojump

-dt 4000

now you will only have 51 frames. more info. check trjconv -h

>
> The trajectory which I read in VMD has 3008 frames and my ligands completely
> disappear after 8 frame (They are not in PBC windows which I checked in
> Graphics -> Graphical Representation -> Periodic)
>
> Can you please advise? I think I have to many frames in my trajectory, how
> can I reduce it in trjconv?
>
> Thank you,
>
>
>
> Steven
>
>
> --
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> http://lists.gromacs.org/mailman/listinfo/gmx-users
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Re: [gmx-users] simulation killed

2012-01-30 Thread lina

did you write this script yourself?

On Mon, Jan 30, 2012 at 6:56 PM, murat özçelik  wrote:
> hi! lina my script this please tell me where is wrong...thanks
>
>
> #!/bin/bash
>
> # Set some environment variables
> FREE_ENERGY=/home/mkiytak/Free_Energy1
> echo "Free energy home directory set to $FREE_ENERGY"
>
> MDP=$FREE_ENERGY/MDP
> echo ".mdp files are stored in $MDP"
>
> LAMBDA=0
>
> # A new directory will be created for each value of lambda and
> # at each step in the workflow for maximum organization.
>
Here add:

if [ -d "Lambda_$LAMBDA" ]; then
rm -r Lambda_$LAMBDA
fi

> mkdir Lambda_$LAMBDA
> cd Lambda_$LAMBDA
>
> #
> # ENERGY MINIMIZATION 1: STEEP  #
> #
> echo "Starting minimization for lambda = $LAMBDA..."
>
> mkdir EM_1
> cd EM_1
>
> # Iterative calls to grompp and mdrun to run the simulations
>
> grompp -f $MDP/EM/em_steep_$LAMBDA.mdp -c $FREE_ENERGY/HIS1/solv.gro -p
> $FREE_ENERGY/HIS1/topol.top -o min$LAMBDA.tpr -maxwarn 3
>
> mdrun -nt 8 -deffnm min$LAMBDA
>
>
> # 
> # ENERGY MINIMIZATION 2: L-BFGS #
> #
>
> cd ../
> mkdir EM_2
> cd EM_2
>
> grompp -f $MDP/EM/em_l-bfgs_$LAMBDA.mdp -c ../EM_1/min$LAMBDA.gro -p
> $FREE_ENERGY/HIS1/topol.top -o min$LAMBDA.tpr -maxwarn 3
>
> # Run L-BFGS in serial (cannot be run in parallel)
>
> mdrun -nt 1 -deffnm min$LAMBDA
>
> echo "Minimization complete."
>
>
>
> #
> # NVT EQUILIBRATION #
> #
> echo "Starting constant volume equilibration..."
>
> cd ../
> mkdir NVT
> cd NVT
>
> grompp -f $MDP/NVT/nvt_$LAMBDA.mdp -c ../EM_2/min$LAMBDA.gro -p
> $FREE_ENERGY/HIS1/topol.top -o nvt$LAMBDA.tpr -maxwarn 3

One thing, do you use  define = -DPOSRES in your nvt_0.mdp, if
yes, you need take care where your posre.itp file stored.

>
> mdrun -nt 8 -deffnm nvt$LAMBDA
>
> echo "Constant volume equilibration complete."
>
>
>
> #
> # NPT EQUILIBRATION #
> #
> echo "Starting constant pressure equilibration..."
>
> cd ../
> mkdir NPT
> cd NPT
>
> grompp -f $MDP/NPT/npt_$ LAMBDA.mdp -c ../NVT/nvt$LAMBDA.gro -p

Here "$ LAMBDA" --> "$LAMBDA", no space.

> $FREE_ENERGY/HIS1/topol.top -t ../NVT/nvt$LAMBDA.cpt -o npt$LAMBDA.tpr
> -maxwarn 3
>
> mdrun -nt 8 -deffnm npt$LAMBDA
>
> echo "Constant pressure equilibration complete."
>
>
> #
> # PRODUCTION MD #
> #
> echo "Starting production MD simulation..."
>
> cd ../
> mkdir Production_MD
> cd Production_MD
>
> grompp -f $MDP/Production_MD/md_$LAMBDA.mdp -c ../NPT/npt$LAMBDA.gro -p
> $FREE_ENERGY/HIS1/topol.top -t ../NPT/npt$LAMBDA.cpt -o md$LAMBDA.tpr
> -maxwarn 3
>
>
> mdrun -nt 8 -deffnm md$LAMBDA
>
> echo "Production MD complete."
>
> # End
> echo "Ending. Job completed for lambda = $LAMBDA"
>
>> Date: Mon, 30 Jan 2012 13:54:18 +0800
>
>> Subject: Re: [gmx-users] simulation killed
>> From: lina.lastn...@gmail.com
>> To: gmx-users@gromacs.org
>
>>
>> On Mon, Jan 30, 2012 at 1:18 AM, murat özçelik 
>> wrote:
>> > hi again capacity of my harddisk 600 GB ı try again ..the
>> > program
>> > gave me below message...
>> >
>> > Reading file md0.tpr, VERSION 4.5.4 (single precision)
>> > Starting 8 threads
>> >
>> > NOTE: The load imbalance in PME FFT and solve is 1211%.
>> >   For optimal PME load balancing
>> >   PME grid_x (1152) and grid_y (1152) should be divisible by
>> > #PME_nodes_x (8)
>> >   and PME grid_y (1152) and grid_z (1152) should be divisible by
>> > #PME_nodes_y (1)
>> >
>> >
>> > Making 1D domain decomposition 8 x 1 x 1
>> > starting mdrun 'Protein in water'
>>
>> > 250 steps,   5000.0 ps.
>> > ./job_0.sh: line 95: 15777 Killed   mdrun -nt 8 -deffnm
>>
>> What's inside your job_0.sh?
>>
>> something wrong your script.
>>
>> > md$LAMBDA
>> >
>> > Production MD complete.
>> > Ending. Job completed for lambda = 0
>> > mkiytak@babil:~/JOB1$
>> >
>> >
>> > How can I solve this problemthanks for your help.
>> >
>> >
>> >
>> >
>> >
>> >
>> >
>&

Re: [gmx-users] simulation killed

2012-01-30 Thread lina

On Mon, Jan 30, 2012 at 9:22 PM, Justin A. Lemkul  wrote:
>
>
> lina wrote:
>>
>> did you write this script yourself?
>>
>
> This script appears to be based on one that I provided in the free energy
> tutorial, but there are some differences (including one of the mistakes you

Your tutorials were well-written. I read some of them. but not this one. so ...

> note below).  It would be helpful if the OP explained what these simulations
> were doing, as well as if they are attempting the tutorial or some other
> different system.
>
> -Justin
>
>
>> On Mon, Jan 30, 2012 at 6:56 PM, murat özçelik 
>> wrote:
>>>
>>> hi! lina my script this please tell me where is
>>> wrong...thanks
>>>
>>>
>>> #!/bin/bash
>>>
>>> # Set some environment variables
>>> FREE_ENERGY=/home/mkiytak/Free_Energy1
>>> echo "Free energy home directory set to $FREE_ENERGY"
>>>
>>> MDP=$FREE_ENERGY/MDP
>>> echo ".mdp files are stored in $MDP"
>>>
>>> LAMBDA=0
>>>
>>> # A new directory will be created for each value of lambda and
>>> # at each step in the workflow for maximum organization.
>>>
>> Here add:
>>
>> if [ -d "Lambda_$LAMBDA" ]; then
>>        rm -r Lambda_$LAMBDA
>> fi
>>
>>> mkdir Lambda_$LAMBDA
>>> cd Lambda_$LAMBDA
>>>
>>> #
>>> # ENERGY MINIMIZATION 1: STEEP  #
>>> #
>>> echo "Starting minimization for lambda = $LAMBDA..."
>>>
>>> mkdir EM_1
>>> cd EM_1
>>>
>>> # Iterative calls to grompp and mdrun to run the simulations
>>>
>>> grompp -f $MDP/EM/em_steep_$LAMBDA.mdp -c $FREE_ENERGY/HIS1/solv.gro -p
>>> $FREE_ENERGY/HIS1/topol.top -o min$LAMBDA.tpr -maxwarn 3
>>>
>>> mdrun -nt 8 -deffnm min$LAMBDA
>>>
>>>
>>> # 
>>> # ENERGY MINIMIZATION 2: L-BFGS #
>>> #
>>>
>>> cd ../
>>> mkdir EM_2
>>> cd EM_2
>>>
>>> grompp -f $MDP/EM/em_l-bfgs_$LAMBDA.mdp -c ../EM_1/min$LAMBDA.gro -p
>>> $FREE_ENERGY/HIS1/topol.top -o min$LAMBDA.tpr -maxwarn 3
>>>
>>> # Run L-BFGS in serial (cannot be run in parallel)
>>>
>>> mdrun -nt 1 -deffnm min$LAMBDA
>>>
>>> echo "Minimization complete."
>>>
>>>
>>>
>>> #
>>> # NVT EQUILIBRATION #
>>> #
>>> echo "Starting constant volume equilibration..."
>>>
>>> cd ../
>>> mkdir NVT
>>> cd NVT
>>>
>>> grompp -f $MDP/NVT/nvt_$LAMBDA.mdp -c ../EM_2/min$LAMBDA.gro -p
>>> $FREE_ENERGY/HIS1/topol.top -o nvt$LAMBDA.tpr -maxwarn 3
>>
>>
>> One thing, do you use  define         = -DPOSRES in your nvt_0.mdp, if
>> yes, you need take care where your posre.itp file stored.
>>
>>> mdrun -nt 8 -deffnm nvt$LAMBDA
>>>
>>> echo "Constant volume equilibration complete."
>>>
>>>
>>>
>>> #
>>> # NPT EQUILIBRATION #
>>> #
>>> echo "Starting constant pressure equilibration..."
>>>
>>> cd ../
>>> mkdir NPT
>>> cd NPT
>>>
>>> grompp -f $MDP/NPT/npt_$ LAMBDA.mdp -c ../NVT/nvt$LAMBDA.gro -p
>>
>>
>> Here "$ LAMBDA" --> "$LAMBDA", no space.
>>
>>> $FREE_ENERGY/HIS1/topol.top -t ../NVT/nvt$LAMBDA.cpt -o npt$LAMBDA.tpr
>>> -maxwarn 3
>>>
>>> mdrun -nt 8 -deffnm npt$LAMBDA
>>>
>>> echo "Constant pressure equilibration complete."
>>>
>>>
>>> #
>>> # PRODUCTION MD #
>>> #
>>> echo "Starting production MD simulation..."
>>>
>>> cd ../
>>> mkdir Production_MD
>>> cd Production_MD
>>>
>>> grompp -f $MDP/Production_MD/md_$LAMBDA.mdp -c ../NPT/npt$LAMBDA.gro -p
>>> $FREE_ENERGY/HIS1/topol.top -t ../NPT/npt$LAMBDA.cpt -o md$LAMBDA.tpr
>>> -maxwarn 3
>>>
>>>
>>> mdrun -nt 8 -deffnm md$LAMBDA
>>>
>>> echo "Production MD complete."
>>>
>>> # End
>>> echo "Ending. Job completed for lambda = $LAMBDA"
>>>
>>&

Re: [gmx-users] Minimization Problems

2012-02-01 Thread lina

On Thu, Feb 2, 2012 at 12:36 PM, Alex Seling  wrote:
> Hello,
>
> I've recently been having trouble with my simulations blowing up.
> Specifically,
>
> "This usually means your system is exploding,
> if not, you should increase table-extension in your mdp file
> or with user tables increase the table size"
>
> for a few interactions, with each of them approaching inf.
>
> Can anyone find anything glaringly wrong with my .mdp?
>
> Thanks,
> Alex Seling
>
> title = Minimization of alpha-synuclein
> cpp = /lib/cpp -traditional
> define = -DFLEXIBLE
> integrator = sd
> constraints = none
> tinit = 0
> dt = 0.001
> nsteps = 100
> emtol = 0.1
> emstep = 0.1
> nstcgsteep = 1000
> bd-fric = 0
> nstlog = 50
> nstenergy = 1
> gen_temp = 273
> gb_epsilon_solvent = 78.3
> implicit_solvent = GBSA
> gb_algorithm = Still
> nstcomm = 10
> xtc_precision = 1000
> gen_vel = yes
> nstxtcout = 0
> nstxout = 100
> pbc = no
> energygrps = system
> nstfout = 0
> nstvout = 0
> niter = 20
> nstlist = 10

it's more about your .gro file (system), less about the .mdp file.

>
> --
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> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
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Re: [gmx-users] reg. error

2012-02-02 Thread lina

On Fri, Feb 3, 2012 at 12:54 PM, Vishwambhar Bhandare
 wrote:
> Hello,
> I am getting error given below,
> wht we can do for this?
>
>
> Program pdb2gmx, VERSION 4.5.4
> Source code file: /build/buildd/gromacs-4.5.4/src/kernel/pdb2gmx.c, line:
> 655
>
> Fatal error:
> Atom 'H5T in residue A 1 was not found in rtp entry RA5 with 31 atoms
> while sorting atoms.

Pay attention to check the residue A 1 in your input .gro file, and
then check the .rtp file in the
some_path_to/share/gromacs/top/_your_choice_of_force_field/rtp file.
> .
>
> Thanks and Regards,
> --
> Vishwambhar
> Centre for Bioinformatics
> Pondicherry University
> Pondicherry
> --
>
>
>
> --
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Re: [gmx-users] trjconv select group

2012-02-03 Thread lina


On Friday 03,February,2012 09:56 PM, francesca vitalini wrote:

Yes but those tips are not for bash scripts... :(


You'd better post what you have done so far about this script,

probably someone can help you improve or refine it.






2012/2/3 Mark Abraham mailto:mark.abra...@anu.edu.au>>

On 4/02/2012 12:21 AM, francesca vitalini wrote:

Hi!
I have to use the gromacs command trjconv to obtain a .gro file
from a .xtc and a .pdb file. I have to do it for several files
in a bash for loop so I'd rather prefer to find a way to make my
script type in the trjconv interactive terminal always the same
number for the system. Any tips?


Check out
http://www.gromacs.org/__Documentation/How-tos/Using___Commands_in_Scripts


Mark

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Re: [gmx-users] trjconv select group

2012-02-03 Thread lina


On Friday 03,February,2012 10:02 PM, francesca vitalini wrote:

Sure!
My code is

#!/bin/bash
for ((i=1; i<=357; i=$i+3))
do
trjconv -f ../xtc/300-${i}.xtc -s ../../dynamin_dimer_phfitted.pdb -o
../cg_gro/300-${i}.gro -pbc whole



try touch a file as index.txt and put 0 in the index.txt

trjconv -f ../xtc/300-${i}.xtc -s ../../dynamin_dimer_phfitted.pdb -o 
../cg_gro/300-${i}.gro -pbc < index.txt



done

very stupidly I just need to type 0 all the time in the interactive
window that trjconv opens.
Any help?







Thanks

2012/2/3 lina mailto:lina.lastn...@gmail.com>>

On Friday 03,February,2012 09:56 PM, francesca vitalini wrote:

Yes but those tips are not for bash scripts... :(


You'd better post what you have done so far about this script,

probably someone can help you improve or refine it.





2012/2/3 Mark Abraham mailto:mark.abra...@anu.edu.au>
<mailto:mark.abra...@anu.edu.__au <mailto:mark.abra...@anu.edu.au>>>


On 4/02/2012 12:21 AM, francesca vitalini wrote:

Hi!
I have to use the gromacs command trjconv to obtain a
.gro file
from a .xtc and a .pdb file. I have to do it for several
files
in a bash for loop so I'd rather prefer to find a way to
make my
script type in the trjconv interactive terminal always
the same
number for the system. Any tips?


Check out

http://www.gromacs.org/Documentation/How-tos/Using_Commands_in_Scripts

<http://www.gromacs.org/__Documentation/How-tos/Using___Commands_in_Scripts>


<http://www.gromacs.org/__Documentation/How-tos/Using___Commands_in_Scripts

<http://www.gromacs.org/Documentation/How-tos/Using_Commands_in_Scripts>>

Mark

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Re: [gmx-users] Problem with simulation of Protein-DNA complex

2012-02-09 Thread lina

On Thu, Feb 9, 2012 at 8:44 PM,   wrote:
> Dear Gromacs users,
>
> I have been trying to simulate a Protein-DNA complex using gromacs, but each
> time I have been facing problems. I would like to point out that both the
> Protein and DNA have been modeled and after that docked in order to obtain a
> complex. Following are the parameters I am using:
>
> Force-Field: amber99sb-ildn
> water model: TIP3P
>
> 40 NA ions were added in order to neutralise the complex-solvent system.
> Gromacs doesn't show any error up until I proceed to do nvt equilibriation.

Before the NVT, you may do some energy minimization.


> Following is nvt.mdp:
>
> title           = PFV_DNA_NVT
> define          = -DPOSRES      ; position restrain the protein
> ; Run parameters
> integrator      = md            ; leap-frog integrator
> nsteps          = 100       ; 2 * 5 = 100 ps
> dt              = 0.001         ; 2 fs
> ; Output control
> nstxout         = 100           ; save coordinates every 0.2 ps
> nstvout         = 100           ; save velocities every 0.2 ps
> nstenergy       = 100           ; save energies every 0.2 ps
> nstlog          = 100           ; update log file every 0.2 ps
> ; Bond parameters
> continuation    = no            ; first dynamics run
> constraint_algorithm = lincs    ; holonomic constraints
> constraints     = all-bonds     ; all bonds (even heavy atom-H bonds)
> constrained
> lincs_iter      = 1             ; accuracy of LINCS
> lincs_order     = 4             ; also related to accuracyi
> ; Neighborsearching
> ns_type         = grid          ; search neighboring grid cels
> nstlist         = 5             ; 10 fs
> rlist           = 1.0           ; short-range neighborlist cutoff (in nm)
> rcoulomb        = 1.0           ; short-range electrostatic cutoff (in nm)
> rvdw            = 1.0           ; short-range van der Waals cutoff (in nm)
> ; Electrostatics
> coulombtype     = PME           ; Particle Mesh Ewald for long-range
> electrostatics
> pme_order       = 4             ; cubic interpolation
> fourierspacing  = 0.16          ; grid spacing for FFT
> ; Temperature coupling is on
> tcoupl          = V-rescale     ; modified Berendsen thermostat
> tc-grps         = Protein Non-Protein
> tau_t           = 0.1   0.1     ; time constant, in ps
> ref_t           = 300   300     ; reference temperature, one for each group,
> in K
> ; Pressure coupling is off
> pcoupl          = no            ; no pressure coupling in NVT
> ; Periodic boundary conditions
> pbc             = xyz           ; 3-D PBC
> ; Dispersion correction
> DispCorr        = EnerPres      ; account for cut-off vdW scheme
> ; Velocity generation
> gen_vel         = yes           ; assign velocities from Maxwell
> distribution
> gen_temp        = 300           ; temperature for Maxwell distribution
> gen_seed        = -1            ; generate a random seed
>
>
> It generates a tpr, but upon mpirun gives the following error:
>
> starting mdrun 'Protein in water'
> 100 steps,   1000.0 ps.
>
> Step 0, time 0 (ps)  LINCS WARNING
> relative constraint deviation after LINCS:
> rms 0.027514, max 0.979682 (between atoms 3460 and 3461)
> bonds that rotated more than 30 degrees:
>  atom 1 atom 2  angle  previous, current, constraint length
>   3455   3457   65.2    0.1542   0.2535      0.1526
>   3455   3456   33.3    0.1093   0.1322      0.1090
>   3457   3459   72.7    0.1105   0.1739      0.1090
>   3457   3458   65.7    0.1105   0.1588      0.1090
>   3460   3469   78.6    0.1409   0.2693      0.1400
>   3460   3461   78.8    0.1409   0.2772      0.1400
>   3461   3463   75.1    0.1406   0.1489      0.1400
>   3463   3465   37.2    0.1403   0.1756      0.1400
>   3463   3464   40.7    0.1083   0.1408      0.1080
>   3465   3467   35.5    0.1403   0.1733      0.1400
>   3467   3469   74.0    0.1405   0.1373      0.1400
>   3467   3468   42.9    0.1083   0.1433      0.1080
> Wrote pdb files with previous and current coordinates
>
> Step 1, time 0.001 (ps)  LINCS WARNING
> relative constraint deviation after LINCS:
> rms 364940.065742, max 11977066.00 (between atoms 3465 and 3466)
> bonds that rotated more than 30 degrees:
>  atom 1 atom 2  angle  previous, current, constraint length
>   3475   3495  110.8    0.1526 20544.7148      0.1522
>   3475   3477  111.6    0.1529 20544.4336      0.1526
>   3475   3476  108.1    0.1094 20543.1309      0.1090
>   3477   3480   62.8    0.1527   4.6441      0.1526
>   3477   3479   57.5    0.1091   4.5683      0.1090
>   3477   3478   93.6    0.1091   4.6160      0.1090
>   3495   3497  138.1    0.1336   4.9133      0.1335
>   3495   3496   69.6    0.1230   4.9085      0.1229
>   3497   3499   40.2    0.1449   0.2036      0.1449
>   3497   3498   43.8    0.1010   0.1527      0.1010
>   3480   3483   35.6    0.1526   0.1902      0.1526
>   3480   3482   42.2    0.1090   0.1501      0.1090
>   3480   3481   41.7    0.1090   0.1485      0.1090
>   3453   3455   88.7    0.1701 117322.3672      0.14

Re: [gmx-users] how to get the block averaged MSD curve ?

2012-02-09 Thread lina

On Thu, Feb 9, 2012 at 7:25 PM, Kiwoong Kim  wrote:
> Hi,
>
> I have a simulation result from 0 to 50ns after equilibration run.
> I want to divide this data set equally into 10blocks (10ns each) and get
> block averaged MSD curve (average of 10 blocks).

I would try some external software. excel.

>
> It seems that I mange to get block MSD data by using  g_msd -beginfit 0
> -endfit 10, g_msd -beginfit 10 -endfit 20,
> Then the output files are msd1.xvg, msd2.xvg,..,msd10.xvg (10 xvg files)
>
> My question is that how can I get averaged MSD from this outputs??
> It seems that g_analyze is appropriate to do this.
>
> g_analyze -n 10 -av ??
>
> Could anybody tell me how to get averaged MSD using g_analyze (each block
> data has different x values but same length) ?
>
> Another question is that
> what is the difference bwn g_msd and g_analyze -msd ??
> Is there any reference of posting to obtain this information ?
>
>
>
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Re: [gmx-users] Error energy minimization on protein with implicit water

2012-02-09 Thread lina

On Thu, Feb 9, 2012 at 6:17 PM, aiswarya pawar  wrote:
>
> Dear Gromacs users,
>
> I have a MD simulated protein and i take frame from this and remove water
> and add water implicit in the interface and want to do energy minimization
> but while doing the minimization i get errors. The steps followed are-
>
> pdb2gmx -ignh -f 1OC0.pdb -o 1oco.pdb -p 1oco.top -nocmap
> grompp -f minim.mdp -c 1oco.pdb -p 1oco.top -o 1oco.tpr
>
> The minim.mdp file =
>
> ; Lines starting with ';' ARE COMMENTS
> ; Everything following ';' is also comment
>
> title        = Energy Minimization    ; Title of run
>
> ; The following line tell the program the standard locations where to find
> certain files
> cpp        = /lib/cpp    ; Preprocessor
>
> ; Define can be used to control processes
> define  = -DFLEXIBLE
>
> ; Parameters describing what to do, when to stop and what to save
> integrator    = steep        ; Algorithm (steep = steepest descent
> minimization)
> emtol        = 1000.0    ; Stop minimization when the maximum force < 1.0
emtol = 1.0
> kJ/mol
> nsteps        = 5000        ; Maximum number of (minimization) steps to
> perform
> nstenergy    = 1        ; Write energies to disk every nstenergy steps
> energygrps    = System    ; Which energy group(s) to write to disk
>
> ; Parameters describing how to find the neighbors of each atom and how to
> calculate the interactions
> ns_type        = simple      ; Method to determine neighbor list (simple,
> grid)
> coulombtype    = cut-off      ; Treatment of long range electrostatic
> interactions
> rcoulomb    = 1.0        ; long range electrostatic cut-off
> rvdw        = 1.0        ; long range Van der Waals cut-off
> constraints    = none        ; Bond types to replace by constraints
> pbc        = no        ; Periodic Boundary Conditions (yes/no)
>
> I get a note as =
> System has non-zero total charge: -4.96e+00
>
> then i tried using genion step as=
>
> genion -s 1oco.tpr -o 1oco.pdb -pname NA -np 5 -p 1oco.top -g ion.log
>
> then again the grompp step and mdrun .
> but while doing mdrun i get an error as=
>
> Stepsize too small, or no change in energy.
> Converged to machine precision,
> but not to the requested precision Fmax < 1000
>
>
> but here i have given nsteps as 5000 so why does it stop.
> --
> Aiswarya  B Pawar
>
> Project Assistant,
> Bioinformatics Dept,
> Indian Institute of Science
> Bangalore
>
>
>
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[gmx-users] how to extract the x y z

2012-02-21 Thread lina

Hi,

I don't know how to extract the position like the x y z with t or r with t.

Thanks for any suggestions,

Best regards,
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Re: [gmx-users] Implicit solvent - Gromacs 4.5.4

2012-02-28 Thread lina

On Tue, Feb 28, 2012 at 10:07 PM, Steven Neumann  wrote:
> Thank you Vedat!
>
> Why do you use -DFLEXIBLE in md and in em?
> Why dont you use constraint algorithm (LINCS) in your simulation?

Otherwise, the system is easily explode with lots of LINCS warning.

Also thanks Vedat for sharing,

Best regards,

>
> Steven
>
> On Tue, Feb 28, 2012 at 12:14 PM, Vedat Durmaz  wrote:
>>
>>
>> hi steven,
>>
>> i've been simulating a 33 AA peptide for the past two days using implicent
>> solvent in order to achieve a proper folding.
>>
>> i haven't added counterions, however, the systems shows nice results
>> according to what i've expected. the mdrun command (for the extension) for
>> our hardware looks as follows:
>>
>> mpiexec -np 4 mdrun -pd -s md.tpr -append -cpi md.cpt -deffnm md 2>&1
>>
>> and here's the mdp file for the energy minimization:
>>
>> define              =  -DFLEXIBLE
>> constraints         =  none
>> integrator          =  steep
>> dt                  =  0.001    ; ps
>> nsteps              =  3
>> vdwtype             =  cut-off
>> coulombtype         =  cut-off
>> pbc                 =  no
>> nstlist             =  0
>> ns_type             =  simple
>> rlist               =  0       ; this means all-vs-all (no cut-off), which
>> gets expensive for bigger systems
>> rcoulomb            =  0
>> rvdw                =  0
>> comm-mode           =  angular
>> comm-grps           =  Protein
>> optimize_fft        =  yes
>> ;
>> ;       Energy minimizing stuff
>> ;
>> emtol               =  5.0
>> emstep              =  0.01
>> ;
>> ; Implicit solvent
>> ;
>> implicit_solvent    =  GBSA
>> gb_algorithm        =  Still ; HCT ; OBC
>> nstgbradii          =  1
>> rgbradii            =  0   ; [nm] Cut-off for the calculation of the Born
>> radii. Currently must be equal to rlist
>> gb_epsilon_solvent  =  80    ; Dielectric constant for the implicit
>> solvent
>> ; gb_saltconc       =  0     ; Salt concentration for implicit solvent
>> models, currently not used
>> sa_algorithm        =  Ace-approximation
>> sa_surface_tension  = -1
>>
>>
>> and for the md run:
>>
>> define              =  -DPOSRESHELIX ; -DFLEXIBLE -DPOSRES
>> constraints         =  none
>> integrator          =  md
>> dt                  =  0.001   ; ps
>> nsteps              =  10 ; 10 ps = 100 ns
>> nstcomm             =  10
>> nstcalcenergy       =  10
>> nstxout             =  1000     ; frequency to write coordinates to output
>> trajectory
>> nstvout             =  0       ; frequency to write velocities to output
>> trajectory; the last velocities are always written
>> nstfout             =  0       ; frequency to write forces to output
>> trajectory
>> nstlog              =  1000         ; frequency to write energies to log
>> file
>> nstenergy           =  1000     ; frequency to write energies to edr file
>>
>> vdwtype             =  cut-off
>> coulombtype         =  cut-off
>>
>> pbc                 =  no
>>
>> nstlist             =  0
>> ns_type             =  simple
>> rlist               =  0       ; this means all-vs-all (no cut-off), which
>> gets expensive for bigger systems
>> rcoulomb            =  0
>> rvdw                =  0
>>
>> comm-mode           =  angular
>> comm-grps           =  system
>>
>> optimize_fft        =  yes
>>
>> ; V-rescale temperature coupling is on
>> Tcoupl              =  v-rescale
>> tau_t               =  0.1
>> tc_grps             =  system
>> ref_t               =  300
>> ; Pressure coupling is off
>> Pcoupl              =  no
>> ; Generate velocites is on
>> gen_vel             =  yes
>> gen_temp            =  300
>> gen_seed            =  -1
>>
>> ;
>> ; Implicit solvent
>> ;
>> implicit_solvent    =  GBSA
>> gb_algorithm        =  Still ; HCT ; OBC
>> nstgbradii          =  1
>> rgbradii            =  0   ; [nm] Cut-off for the calculation of the Born
>> radii. Currently must be equal to rlist
>> gb_epsilon_solvent  =  80    ; Dielectric constant for the implicit
>> solvent
>> ; gb_saltconc       =  0     ; Salt concentration for implicit solvent
>> models, currently not used
>> sa_algorithm        =  Ace-approximation
>> sa_surface_tension  = -1
>>
>>
>> best regards,
>> vedat
>>
>>
>> Am 28.02.2012 11:59, schrieb Steven Neumann:
>>
>>> Dear Gmx Users,
>>> I am using Gromacs 4.5.4 and I would like to implement implicit solvent
>>> for folding of my protein. I read mailing list and it is still confusing for
>>> me.
>>> Is it proper to use counterions within the system? If not, how can I
>>> obtain netral system?
>>> Do we use cut off for vdw and coulombic interactions?
>>> What kind of integrator should be used with a timestep?
>>> I will appreciate an mdp file for protein folding! Thank you
>>> Steven
>>
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Re: [gmx-users] PBC - Protein and Ligands

2012-02-29 Thread lina

On 1 Mar, 2012, at 1:01, Steven Neumann  wrote:

> Dear Gmx Users,
>  
> I am run a simulation with Gromacs 4.5.4. of my protein and 15 ligands. The 
> problem I face is PBC which I cannot get rid of. I used:
>  
> 1.  First make your molecules whole if you want them whole (system).
> trjconv -f md298SKIP4.xtc -s md298.tpr -pbc whole -o md298whole.xtc
> 2.  Cluster your molecules/particles if you want them clustered
>  
> 3.  Extract the first frame from the trajectory as reference for removing 
> jumps if you want to remove jumps.
> trjconv -f md298.trr -s md298.tpr -dump 0 -o 1stframe.pdb
> 4.  Remove jumps if you want to have them removed using the first frame 
> (system)
> trjconv -f md298whole.xtc -s 1stframe.pdb -pbc nojump -o md298nojump.xtc
>  
> So the trajecory of my ligands is smooth but they do do bind to the different 
> periodic images. As i know it is impossible to obtain the proper trajectory 
> of all of them I just want to obtain the realistic final positions of my 
> system to extract pdb file for further umbrella sampling. Any suggestions?

You may wanna try 

Trjconv -f md298SKIP4.xtc -s md298.tpr -pbc whole -ur compact -o pdbs.pdb -dt 
1000

Please change dt if necessary. 


>  
> Steven
>  
> -- 
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[gmx-users] dssp and gromacs version

2012-03-01 Thread lina

Hi,

is the old dssp not compatible with the gromacs 4.5.5 ?

I am confused,

Thanks,

Best regards,
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Re: [gmx-users] dssp and gromacs version

2012-03-02 Thread lina

On Fri, Mar 2, 2012 at 3:55 PM, Mark Abraham  wrote:
> On 2/03/2012 6:52 PM, lina wrote:
>>
>> Hi,
>>
>> is the old dssp not compatible with the gromacs 4.5.5 ?
>>
>> I am confused,
>>
>> Thanks,
>>
>> Best regards,
>
>
> The new DSSP is not compatible with any GROMACS

Ha ... the dssp complain the segmentation fault in 4.5.5, but can run
smoothly in 4.5.3.

IIRC, seems there were some threads talked about that before.

>
> Mark
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Re: [gmx-users] g_dist without output file

2012-03-10 Thread lina

On Sat, Mar 10, 2012 at 7:14 PM, Atila Petrosian
 wrote:
> Dear all
>
> When I use  g_dist -f *.trr -s *.tpr -n *.ndx -o dist.xvg -dist 0.5,
> program was done without error, but it don't create output file
> (dist.xvg) in the directory in which g_dist tool was run.
>
> What is reason of this case?

Try without the -dist 0.5, you will get the -o dist.xvg output.

the -dist is Print all atoms in group 2 closer than dist to
the center of mass of group 1


>
>
> Any help will highly appreciated.
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Re: [gmx-users] g_dist without output file

2012-03-10 Thread lina

On Sat, Mar 10, 2012 at 9:17 PM, Atila Petrosian
 wrote:
> Dear Lina
>
> Thanks for your reply.
>
> Without the -dist 0.5, I get the -o dist.xvg output, but I need list
> of the all atoms in group 2 closer than dist to the center of mass of
> group 1.

It print on the terminal, you may notice it.

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Re: [gmx-users] g_dist without output file

2012-03-10 Thread lina

On Sat, Mar 10, 2012 at 10:23 PM, Atila Petrosian
 wrote:
> Dear Lina
>
> There is not any things related to list of atoms on the terminal.


t: 100  83 ILE 845 CG1  1.60274 (nm)
t: 100  83 ILE 846 CG2  1.63838 (nm)
t: 100  83 ILE 847 CD  1.59769 (nm)
t: 100  83 ILE 848 C  1.8202 (nm)
t: 100  83 ILE 849 O  1.86972 (nm)
t: 100  84 ALA 850 N  1.88309 (nm)
t: 100  84 ALA 851 H  1.85958 (nm)
t: 100  84 ALA 853 CB  1.99705 (nm)
Last frame 50 time  100.000

gcq#310: "Shoot them the atom now" (The Ramones)

g_dist_g -f try_1.xtc -s try_1.tpr -dt 5 -b 0 -e 100 -dist 2 -n index_1.ndx

>
>
> Best regards
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Re: [gmx-users] g_dist without output file

2012-03-10 Thread lina

On Sat, Mar 10, 2012 at 10:23 PM, Atila Petrosian
 wrote:
> Dear Lina
>
> There is not any things related to list of atoms on the terminal.

Might your distance -dist so large.

try a smaller one and see.
>
>
> Best regards
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Re: [gmx-users] Generating topology

2012-03-21 Thread lina

On Thu, Mar 22, 2012 at 11:54 AM, Spring buds  wrote:
> Hi
>
> A protein sits on the top of another protein (not docking). I then used
> pdb2gmx command to generate the topology. Surprisingly, i got  five files,
> as given below: I think the two proteins are not connected each other. is it
> possible to make it one posre and topol file.

You have already have one posre and topol.top

more topol.top
check what's inside your topol.top. pay attention to "include"
>
> Many thanks in advance
>
> posre_Protein_chain_A.itp
> posre_Protein_chain_A2.itp
> topol.top
> topol_Protein_chain_A.itp
> topol_Protein_chain_A2.itp
>
>
>
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Re: [gmx-users] continue replica exchange MD

2012-03-22 Thread lina

On Wed, Mar 21, 2012 at 11:36 PM, Kukol, Andreas  wrote:
> Hello,
>
> Upon continuing a replica exchange MD simulation using the command
>
> mdrun -cpi state.cpt -append -s tpr_remd20ns_.tpr -multi 48 -replex 1 
> -cpt 60 -x xtcRemd_20ns.xtc -c afterRemd_20ns.gro -g logRemd_20ns.log -v -e 
> edrRemd_20ns.edr -stepout 2000

>From my side, I have no problem resuming or extending the REMD
simulations in V.4.5.5 and 4.5.4

Here is the command:

mdrun_g_f -s md_.tpr -multi 32 -replex 500  -cpi state_.cpt -append

    I use state_.cpt, not state.cpt

>
> I get the following output:
> **
> ...
> ...
> 500 steps,  1.0 ps (continuing from step 49430,     98.9 ps).
> 500 steps,  1.0 ps (continuing from step 49430,     98.9 ps).
>
> step 49430, will finish Wed Sep 12 16:09:33 2012
> step 5, will finish Thu May 24 11:23:04 2012
> Step 47546: resetting all time and cycle counters
>
> =>> PBS: job killed: walltime 604823 exceeded limit 604800
> Terminated
> **
>
> Apparently, the job runs for one week on a computer cluster (that is the 
> maximum time allowed), but it does not progress very much beyond step 49430.
>
> Also the log-file does not show any more steps:
> 
>           Step           Time         Lambda
>          46455       92.91000        0.0
>
> Grid: 18 x 17 x 25 cells
>   Energies (kJ/mol)
>       G96Angle    Proper Dih. Ryckaert-Bell.  Improper Dih.          LJ-14
>    5.83095e+04    3.70277e+04    2.14102e+03    8.83853e+03   -7.33070e+02
>     Coulomb-14        LJ (SR)        LJ (LR)  Disper. corr.   Coulomb (SR)
>    2.29503e+05    3.04138e+05   -2.66781e+04   -8.51221e+03   -2.74692e+06
>   Coul. recip. Position Rest.      Potential    Kinetic En.   Total Energy
>   -9.59421e+05    5.41532e+03   -3.09689e+06    5.18959e+05   -2.57793e+06
>    Temperature Pres. DC (bar) Pressure (bar)   Constr. rmsd
>    2.97550e+02   -1.14933e+02    5.41944e+01    0.0e+00
>
> Writing checkpoint, step 49430 at Fri Jan 27 09:43:23 2012
>
> ---
> Restarting from checkpoint, appending to previous log file.
> ...
> ...
> Started mdrun on node 0 Tue Mar  6 16:40:10 2012
>
>           Step           Time         Lambda
>          49430       98.86000        0.0
>
> Grid: 18 x 17 x 25 cells
>   Energies (kJ/mol)
>       G96Angle    Proper Dih. Ryckaert-Bell.  Improper Dih.          LJ-14
>    5.84241e+04    3.69121e+04    2.09533e+03    8.80916e+03   -4.67086e+02
>     Coulomb-14        LJ (SR)        LJ (LR)  Disper. corr.   Coulomb (SR)
>    2.29528e+05    2.99825e+05   -2.67028e+04   -8.51334e+03   -2.74410e+06
>   Coul. recip. Position Rest.      Potential    Kinetic En.   Total Energy
>   -9.59506e+05    5.47116e+03   -3.09823e+06    5.18993e+05   -2.57923e+06
>    Temperature Pres. DC (bar) Pressure (bar)   Constr. rmsd
>    2.97570e+02   -1.14963e+02    2.67842e+00    0.0e+00
>
>           Step           Time         Lambda
>          5      100.0        0.0
>
>   Energies (kJ/mol)
>       G96Angle    Proper Dih. Ryckaert-Bell.  Improper Dih.          LJ-14
>    5.86161e+04    3.71585e+04    2.15336e+03    8.92946e+03   -4.84684e+02
>     Coulomb-14        LJ (SR)        LJ (LR)  Disper. corr.   Coulomb (SR)
>    2.29950e+05    3.01014e+05   -2.66724e+04   -8.51306e+03   -2.74349e+06
>   Coul. recip. Position Rest.      Potential    Kinetic En.   Total Energy
>   -9.59537e+05    5.56712e+03   -3.09531e+06    5.19371e+05   -2.57594e+06
>    Temperature Pres. DC (bar) Pressure (bar)   Constr. rmsd
>    2.97787e+02   -1.14956e+02    2.36460e+01    1.50068e-05
> [End of log-file]
> ***
>
> I wonder, if this is my mistake (using the mdrun wrongly), a Gromacs problem 
> or maybe a problem of the computer cluster (MPI, etc). I would be grateful 
> for any help.
>
> Many thanks
> Andreas--
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Re: [gmx-users] em fatal error!

2012-04-02 Thread lina

On Mon, Apr 2, 2012 at 5:27 PM, ankita oindrila  wrote:
> We are trying to do simulation of lysozyme in water.
>
> step with problem : energy minimization.
>
> command given: [root@localhost gromacs-4.0.5]# grompp -f minim.mdp -c
> 1AKI_solv_ions.gro -p topol.top -o em.tpr
>
>  :-)  G  R  O  M  A  C  S  (-:
>
>     Getting the Right Output Means no Artefacts in Calculating Stuff
>
>     :-)  VERSION 4.0.5  (-:
>
>
>   Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
>    Copyright (c) 1991-2000, University of Groningen, The Netherlands.
>  Copyright (c) 2001-2008, The GROMACS development team,
>     check out http://www.gromacs.org for more information.
>
>  This program is free software; you can redistribute it and/or
>   modify it under the terms of the GNU General Public License
>  as published by the Free Software Foundation; either version 2
>  of the License, or (at your option) any later version.
>
>     :-)  grompp  (-:
>
> Option Filename  Type Description
> 
>   -f  minim.mdp  Input, Opt!  grompp input file with MD parameters
>  -po  mdout.mdp  Output   grompp input file with MD parameters
>   -c 1AKI_solv_ions.gro  Input    Structure file: gro g96 pdb tpr tpb
> tpa
>   -r   conf.gro  Input, Opt.  Structure file: gro g96 pdb tpr tpb tpa
>  -rb   conf.gro  Input, Opt.  Structure file: gro g96 pdb tpr tpb tpa
>   -n  index.ndx  Input, Opt.  Index file
>   -p  topol.top  Input    Topology file
>  -pp  processed.top  Output, Opt. Topology file
>   -o em.tpr  Output   Run input file: tpr tpb tpa
>   -t   traj.trr  Input, Opt.  Full precision trajectory: trr trj cpt
>   -e   ener.edr  Input, Opt.  Energy file: edr ene
>
> Option   Type   Value   Description
> --
> -[no]h   bool   no  Print help info and quit
> -nice    int    0   Set the nicelevel
> -[no]v   bool   yes Be loud and noisy
> -time    real   -1  Take frame at or first after this time.
> -[no]rmvsbds bool   yes Remove constant bonded interactions with virtual
>     sites
> -maxwarn int    0   Number of allowed warnings during input
> processing
> -[no]zero    bool   no  Set parameters for bonded interactions without
>     defaults to zero instead of generating an error
> -[no]renum   bool   yes Renumber atomtypes and minimize number of
>     atomtypes
>
>
> Back Off! I just backed up mdout.mdp to ./#mdout.mdp.1#
> checking input for internal consistency...
> processing topology...
> Opening library file /usr/local/gromacs/share/gromacs/top/ffoplsaa.itp
> Opening library file /usr/local/gromacs/share/gromacs/top/ffoplsaanb.itp
> Opening library file /usr/local/gromacs/share/gromacs/top/ffoplsaabon.itp
> Generated 332520 of the 332520 non-bonded parameter combinations
> Generating 1-4 interactions: fudge = 0.5
> Generated 332520 of the 332520 1-4 parameter combinations
> Opening library file /usr/local/gromacs/share/gromacs/top/spce.itp
> Opening library file /usr/local/gromacs/share/gromacs/top/ions.itp
> Excluding 3 bonded neighbours molecule type 'Protein_A'
> Excluding 2 bonded neighbours molecule type 'SOL'
>
> ---
> Program grompp, VERSION 4.0.5

You use Version 4.0.5.

If I remember correctly, the earlier version has different pname.
(seems one is NA+, one is NA)

If I were you, I would update to latest version and try.

> Source code file: toppush.c, line: 1641
>
> Fatal error:
> No such moleculetype NA
>
> what should we do
>
>
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[gmx-users] how to change the timestamp of a xtc file

2012-04-05 Thread lina

Hi,

A quick question, how can I change the .xtc file which beginning at 0,
end at 1 ns to beginning at 5ns and end at 6ns.

Thanks for any suggestions,

Best regards,
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Re: [gmx-users] how to change the timestamp of a xtc file

2012-04-05 Thread lina

On Thu, Apr 5, 2012 at 4:42 PM, Peter C. Lai  wrote:
> trjcat -settime or trjconv -t0

Thank you, a further question, a trjcat-ed  xtc file, which timestamp like

0-5 0-2 0-5 0-3 ...

Are there someway to update them all in the trjcated ones?

Thanks ahead,

>
> On 2012-04-05 03:59:44PM +0800, lina wrote:
>> Hi,
>>
>> A quick question, how can I change the .xtc file which beginning at 0,
>> end at 1 ns to beginning at 5ns and end at 6ns.
>>
>> Thanks for any suggestions,
>>
>> Best regards,
>> --
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> --
> ==
> Peter C. Lai                    | University of Alabama-Birmingham
> Programmer/Analyst              | KAUL 752A
> Genetics, Div. of Research      | 705 South 20th Street
> p...@uab.edu                     | Birmingham AL 35294-4461
> (205) 690-0808                  |
> ==
>
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Re: [gmx-users] which xtc file should be used for the trjconv command

2012-04-05 Thread lina

On Thu, Apr 5, 2012 at 11:50 AM, Acoot Brett  wrote:
> Dear All,
>
> In the on-line tutorial on lysozyme
> (http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/09_analysis.html),
> there is a command
>
> trjconv -s md_0_1.tpr -f md_0_1.xtc -o md_0_1_noPBC.xtc -pbc mol -ur compact
>
> Will you please consider in that command whether we can change md_1_1.xtc to
> state.xtc?

Yes.

>
> I am looking forward to getting your reply.
>
> Cheers,
>
> Acoot
>
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[gmx-users] something about tpr file

2012-04-05 Thread lina

Hi,

suppose I lost original .tpr file,

can I get tpr file from the .xtc file ? I mean from the .xtc or trr
file, not by re-run grompp to generate tpr file.

Thanks ahead,

Best regards,
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Re: [gmx-users] how to change the timestamp of a xtc file

2012-04-05 Thread lina

On Thu, Apr 5, 2012 at 6:07 PM, Mark Abraham  wrote:
>
>
> On 05/04/12, lina  wrote:
>
> On Thu, Apr 5, 2012 at 4:42 PM, Peter C. Lai  wrote:
>> trjcat -settime or trjconv -t0
>
> Thank you, a further question, a trjcat-ed  xtc file, which timestamp like
>
> 0-5 0-2 0-5 0-3 ...
>
> Are there someway to update them all in the trjcated ones?
>
>
> I've no idea what you mean, but trjconv -settime is still your friend.

sorry I didn't say it clearly.

Well, I mean several xtc files
all starts with 0
but ends with 1 ns, 2 ns, 1 ns

I use trjcat -cat combine them together. now I wonder can make the
time continuously.

from 0 to 4ns.

Thanks,


>
> Mark
>
>
>
>
> Thanks ahead,
>
>>
>> On 2012-04-05 03:59:44PM +0800, lina wrote:
>>> Hi,
>>>
>>> A quick question, how can I change the .xtc file which beginning at 0,
>>> end at 1 ns to beginning at 5ns and end at 6ns.
>>>
>>> Thanks for any suggestions,
>>>
>>> Best regards,
>>> --
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>>
>> --
>> ==
>> Peter C. Lai                    | University of Alabama-Birmingham
>> Programmer/Analyst              | KAUL 752A
>> Genetics, Div. of Research      | 705 South 20th Street
>> p...@uab.edu                     | Birmingham AL 35294-4461
>> (205) 690-0808                  |
>> ==
>>
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Re: [gmx-users] the different protonation state of HIS

2012-04-05 Thread lina

On Thu, Apr 5, 2012 at 7:14 PM, Acoot Brett  wrote:
> Dear All,
>
> For the different protonation state of HIS, what are there 3-letter code for
> GROMACS? And how about -SH and -S-S- codon? Or do you have a web link for me
> to read? Do we still have any other confusing amino acids?

In pdb2gmx -his

you will get something like below

0. H on ND1 only (HSD)
1. H on NE2 only (HSE)
2. H on ND1 and NE2 (HSP)
3. Coupled to Heme (HIS1)

Then based on the pka value and the PH, you can make a choice.

>
> I am looking forward to getting a reply from you.
>
> Cheers,
>
> Acoot
>
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Re: [gmx-users] Protein ligand molecular dynamics simulation

2012-04-16 Thread lina

On Mon, Apr 16, 2012 at 11:01 PM, sai nitin  wrote:
> Hi all,
>
> I have done complex (protein + ligand) complex from autodock software using
> this complex im trying to follow
>
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex/01_pdb2gmx.html
> tutorial
>
> But when i take complex structure directly from autodock result and run
> PDB2GMX it will give error because it is not recognizing ligand topology
> which is in complex structure.
> Then i followed justin tutorial took protein alone and applied Charmm27
> Force field and used generate ligand topologies using Swissparam tool
> (http://swissparam.ch/) when i do Editconf and created cubic box ligand is
> going away from protein.
>
> Actually my main task to place ligand in paraticular binding site in my
> protein and perform molecular dynamics.
>
> Can any body tell me how to do this..?

1] pdb2gmx generate ligands.top (if possible, basically you need
generate your ligand.itp by other ways) and rename it as ligands.itp
2] pdb2gmx generate protein.top and rename it as protein.itp (also
need delete some entry)
3] create the topol.top includes the ligands.itp and protein.itp, take
care the double entry.
(To make it easy, you may take some pdb with several chains. use
pdb2gmx and see how those top files combined together.)
4] The docked structure skip the pdb2gmx step. go directly to the editconf.

You may do a try, but it will be helpful if you are a bit familiar
with how to combine those top_files.

>
>
> Thanks in advance
>
> --
>
> Sainitin D
>
>
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Re: [gmx-users] g_tcaf segmentation fault

2012-09-26 Thread lina

On Wednesday 26,September,2012 06:33 PM, Stelios Karozis wrote:
> Dear all,
> 
> I am attempting to calculate the viscosity of a liquid binary system of
> 500 molecules (3050 atoms), via g_tcaf command.
> The system is equilibrated. The list of command I use is:
> 
> /g_covar -f traj.trr -s topol.tpr -n index.ndx -o eigenval.xvg -v
> eigenvec.trr -av average.pdb -l covar.log//
> //g_tcaf -b 0 -e 2 -dt 0.001 -f eigenvec.trr -s topol.tpr -n
> index.ndx -mol -oc tcaf_cub.xvg  -oa tcaf_all.xvg -o tcaf.xvg -of
> tcaf_fit.xvg/

-dt 0.001 ?

> 
> The result is a Segmentation fault error:
> 
> /Selected 0: 'System'//
> //trn version: GMX_trn_file (single precision)//
> //Last frame -1 time0.000/*/
> /**/Segmentation fault/*
> 
> I use GROMACS 4.5.5
> 
> What am I doing wrong?
> 
> Thanks in advance
> Stelios
> 

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Re: [gmx-users] g_tcaf segmentation fault

2012-09-26 Thread lina

On Thursday 27,September,2012 12:13 AM, Stelios Karozis wrote:
> The -dt flag is the time step between the frames in ps. I tried the command 
> in any combination i could think of. With -dt without, with -b without, and 
> so on. The only way i get a partial result is to use the .trr file from the 
> simulation and not from the g_covar command and even then i get the density 
> of the system and after that "segmentation fault"
> 

Segmentation fault involves lots.
If I were you, I would try -dt 100 or large to reduce memory
requirement. or perhaps try the very short time period. namely -e 200 to
see what's going on.

> Ο χρήστης lina  έγραψε:
> 
> On Wednesday 26,September,2012 06:33 PM, Stelios Karozis wrote:
>> Dear all,
>>
>> I am attempting to calculate the viscosity of a liquid binary system of
>> 500 molecules (3050 atoms), via g_tcaf command.
>> The system is equilibrated. The list of command I use is:
>>
>> /g_covar -f traj.trr -s topol.tpr -n index.ndx -o eigenval.xvg -v
>> eigenvec.trr -av average.pdb -l covar.log//
>> //g_tcaf -b 0 -e 2 -dt 0.001 -f eigenvec.trr -s topol.tpr -n
>> index.ndx -mol -oc tcaf_cub.xvg  -oa tcaf_all.xvg -o tcaf.xvg -of
>> tcaf_fit.xvg/
> 
> -dt 0.001 ?
> 
>>
>> The result is a Segmentation fault error:
>>
>> /Selected 0: 'System'//
>> //trn version: GMX_trn_file (single precision)//
>> //Last frame -1 time0.000/*/
>> /**/Segmentation fault/*
>>
>> I use GROMACS 4.5.5
>>
>> What am I doing wrong?
>>
>> Thanks in advance
>> Stelios
>>
> 

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Re: [gmx-users] g_tcaf segmentation fault

2012-09-26 Thread lina

On Thursday 27,September,2012 12:55 AM, Stelios Karozis wrote:
> Thanks for the suggestion.
> I just tried and the problem presists. 
> Just to be clear, the right way is to use the g_covar.trr file, correct? 

 -f   traj.trr  InputFull precision trajectory: trr trj cpt

Here the full precision means double precision? I see you use single
precision.

I have never tried this one, perhaps someone else may give you some
suggestions.

Best regards,

> 
> Ο χρήστης lina  έγραψε:
> 
> On Thursday 27,September,2012 12:13 AM, Stelios Karozis wrote:
>> The -dt flag is the time step between the frames in ps. I tried the command 
>> in any combination i could think of. With -dt without, with -b without, and 
>> so on. The only way i get a partial result is to use the .trr file from the 
>> simulation and not from the g_covar command and even then i get the density 
>> of the system and after that "segmentation fault"
>>
> 
> Segmentation fault involves lots.
> If I were you, I would try -dt 100 or large to reduce memory
> requirement. or perhaps try the very short time period. namely -e 200 to
> see what's going on.
> 
>> Ο χρήστης lina  έγραψε:
>>
>> On Wednesday 26,September,2012 06:33 PM, Stelios Karozis wrote:
>>> Dear all,
>>>
>>> I am attempting to calculate the viscosity of a liquid binary system of
>>> 500 molecules (3050 atoms), via g_tcaf command.
>>> The system is equilibrated. The list of command I use is:
>>>
>>> /g_covar -f traj.trr -s topol.tpr -n index.ndx -o eigenval.xvg -v
>>> eigenvec.trr -av average.pdb -l covar.log//
>>> //g_tcaf -b 0 -e 2 -dt 0.001 -f eigenvec.trr -s topol.tpr -n
>>> index.ndx -mol -oc tcaf_cub.xvg  -oa tcaf_all.xvg -o tcaf.xvg -of
>>> tcaf_fit.xvg/
>>
>> -dt 0.001 ?
>>
>>>
>>> The result is a Segmentation fault error:
>>>
>>> /Selected 0: 'System'//
>>> //trn version: GMX_trn_file (single precision)//
>>> //Last frame -1 time0.000/*/
>>> /**/Segmentation fault/*
>>>
>>> I use GROMACS 4.5.5
>>>
>>> What am I doing wrong?
>>>
>>> Thanks in advance
>>> Stelios
>>>
>>
> 

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Re: [gmx-users] DNA orientation restrain

2012-10-01 Thread lina

On Monday 01,October,2012 01:44 PM, 仝督读 wrote:
> Hi everyone,
> 
> I am doing a DNA simulation in a long simulation box (the lengthen of z is
> much larger than x and y). So I want to constrain the DNA molecule lying
> along the z axis. But I don't know how to realize this in GROMACS.
> 
> Actually I notice there is orientation restraints in 4.3.5 of GMX Manual.
> But the orientation value is set to be observables of NMR experiments, such
> as this example:
> ; ai aj type exp. label alpha const. obs. weight
> 31 32 1  1  3  3  6.083  -6.73  1.0
> But how can I set the observable in my case as it's not an NMR experiment?
> 
> Any suggestion will be appreciate.
> Thanks very much

Dudu,

notice the posre.itp?

; atom  type  fx  fy  fz
 1 1  1000  1000  1000
 5 1  1000  1000  1000


change the fz value to be high enough, like below:

1 1  1000  1000  5

this 5 I just made up here as example, you may try to pick a
reasonable one.
> 
> Dudu Tong
> <31%2032%201%201%203%203>

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Re: [gmx-users] Mopac/Gmx QMMM

2011-07-07 Thread lina

I did not try before,

but I guess that you might need install at least the libs of mopac7,

try apt-get install libmopac7-dev

or better search your repository, there are .deb avaiable.


On Thu, Jul 7, 2011 at 11:37 AM, Yao Yao  wrote:

> I am trying to compile mopac with gmx for qmmm calculation purpose and
> found the link
> http://www.gromacs.org/Downloads/Installation_Instructions/compiling_QMMM
> is really helpful.
>
> However I can only download the on of the two required fortran files,
> gmxmop.f,
> but not the other, dcart.f. And since I am using linux, I would like to
> download libmopac.a,
> which is not available on the webpage.
>
> Could anyone share these files with me? I really appreciate it.
>
> Best,
>
> Yao
>
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lina
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Re: [gmx-users] help on mdrun

2011-07-09 Thread lina

I am not sure I can give an affirmative working answer, but you may check

ssh to each node, use "top" to see whether it's really run or just
occupy the node but not use.



On Sat, Jul 9, 2011 at 8:56 AM, Mark Abraham  wrote:
> On 9/07/2011 3:37 AM, raghu...@bcpindia.org wrote:
>>
>> Hi
>>
>>
>> I have a problem related to submitting a mdrun job on cluster.  I tried to
>> ask help or gromacs and rocks users-group.
>>
>> My machine specs.
>> Cluster of Intel Xeon processors:QC with Rocks Cluster.  8 processors (16
>> threads)
>>
>> When I submit mdrun -deffnm umbrella0 -pf pullf-umbrella0.xvg -px
>> pullx-umbrella0.xvg on the localhost, the job takes note of 16 threads and
>> the job completes in a day.  But when I try submitting it to the cluster
>> using following qsub script the job takes ~16 days
>>
>> ---
>> #!/bin/bash
>> #
>> #$ -cwd
>> #$ -S /bin/bash
>> #
>> #$ -N umbrella0
>> #$ -e umbrella0.errout
>> #$ -o umbrella0.out
>> #
>> #$ -pe mpi 16
>>
>> echo -n "Running on: "
>>
>> /opt/openmpi/bin/mpirun -np 16 -machinefile /home/raghuvir/machines
>> /share/apps/gromacs-4.5.3/bin/mdrunmpi -deffnm umbrella0 -pf
>> pullf-umbrella0.xvg -px pullx-umbrella0.xvg
>>
>> echo "Done."
>> ---
>
> That's fine as far as GROMACS is concerned, so long as mdrunmpi really has
> been compiled with MPI. You can get what diagnostic information it knows
> about the MPI setup from the very top of the .log file. Otherwise, you'll
> have troubleshoot your use of MPI and your batch queue system.
>
> Mark
> --
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Re: [gmx-users] restarting stopped mdrun

2011-07-11 Thread lina

extend  "!=" restart

In your situation, no need tpbconv,

Just

mdrun -deffnm md -cpi md.cpt -append


On Mon, Jul 11, 2011 at 4:35 PM, Mohana lakshmi  wrote:
>
>
> - Forwarded Message 
> From: Mohana lakshmi 
> To: gmx-users-requ...@gromacs.org
> Sent: Mon, 11 July, 2011 1:53:04 PM
> Subject: restarting stopped mdrun
>
> Dear all,
>
> I kept mdrun run for 3ns but the job stopped when it reached 1263999 steps
> due to system shut down. I used tpbconv command (tpbconv -f md.trr -s md.tpr
> -e md.edr -extend 474 -o md2.trr and  mdrun -s md.tpr -cpi md.cpt) to
> restart my job but i got this error - Fatal error:
> File appending requested, but only 1 of the 4 output files are present.
>
> Please help me to figure out where i did mistake.
>
>
> Thank you
>
> N. Mohanalakshmi
>
>
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Re: [gmx-users] Gromacs on IBM clusters

2011-07-12 Thread lina

On Wed, Jul 13, 2011 at 12:21 AM, Justin A. Lemkul  wrote:
>
>
> Kavyashree M wrote:
>>
>> Dear users,
>>
>> I was trying to run gromacs-4.5.3 in IBMcluster using mpich-1.2.7
>> rather than openmpi. But I was getting some error. Sorry I donot
>> remember the error. But Is it possible to run gromacs-4.5.3 using
>> mpich implementation?

I guess yes.

I checked version 4.5.3 (why you don't try V4.5.4?) since I am not so
sure about the difference of openmpi and mpich.

./configure --help

  --enable-mpiCompile for parallel runs using MPI (instead of
  threads)
  --enable-mpi-environment=VAR
  Only start parallel runs when VAR is set
  --disable-mpi-in-place  Disable MPI_IN_PLACE. For MPI implementations that
  have broken support for it (some versions of MPICH,
  for example).

"(some versions of MPICH, for example)."
so my none-knowledge-based guess is that it supports.


>>
>
> Probably, but without an actual error message and a complete description
> (including commands - configuration? compilation? running mdrun?) of what
> you were doing when the error occurred, you're not going to get any useful
> assistance.
>
> -Justin
>
> --
> 
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> 
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Re: [gmx-users] Weird problem

2011-07-15 Thread lina

There might be relevant to walltime settings. There might be a default limit.

try qsub -l walltime=1000:00:00 yourjob

adjust the time or google further to meet your need.


On Fri, Jul 15, 2011 at 2:27 AM, Justin A. Lemkul  wrote:
>
>
> Sayan Bagchi wrote:
>>
>> Hello All,
>> I am having a weird problem and I do not know whether it has to do
>> anything with Gromacs or the cluster setting I am using.
>> When I run a MD simulation (on any protein), the job automatically
>> terminates overnight without an error message. I mean if I start the job
>> early in the morning it runs longer than if I start the job later in the
>> day. But it never runs to the desired length mentioned in the .mdp file.
>>
>
> If you are not receiving any error messages from Gromacs, then it is
> something your system is doing that is unrelated to mdrun.  Contact your
> system administrators.  Some queues employ systems to purge jobs after a
> certain amount of time or even stop all jobs at a certain time of day to
> allow other jobs to start.
>
> -Justin
>
>> I am copying the .mdp file:
>>
>> -
>>
>> integrator      = md
>> nsteps          = 500
>> dt              = 0.002
>> nstlist         = 10
>> nstcomm         = 1
>> rlist           = 1.0
>> coulombtype     = pme
>> rcoulomb        = 1.0
>> vdw-type        = cut-off
>> rvdw            = 1.0
>> tcoupl          = Nose-Hoover
>> tc-grps         = protein non-protein
>> tau-t           = 0.5 0.5
>> ref-t           = 298 298
>> Pcoupl              =  Parrinello-Rahman
>> pcoupltype          =  isotropic
>> tau_p               =  1.0
>> compressibility     =  4.5e-5
>> ref_p               =  1.0
>> nstxout         = 100
>> nstvout         = 100
>> nstxtcout       = 100
>> nstenergy       = 100
>> userint1        = 123
>> userint2        = 124
>> userint3        = 247
>> ---
>>
>> Any thoughts?
>>
>> Sayan.
>>
>>
>>
>
> --
> 
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
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[gmx-users] How to examine the problem of one atom during EM

2011-07-27 Thread lina

Hi,

Form the begining to 5 steps, during EM, all exit in atom 8524,
how do I check it further? I mean, from which parts to examine?
I also switched to double version to run the EM.


Step=42296, Dmax= 2.9e-10 nm, Epot= -2.17267e+05 Fmax= 1.49514e+04, atom= 8524
...
Step=42313, Dmax= 2.0e-10 nm, Epot= -2.17267e+05 Fmax= 2.23506e+04, atom= 8524
...
Step=5, Dmax= 1.7e-10 nm, Epot= -2.17267e+05 Fmax= 2.89751e+04, atom= 8524

writing lowest energy coordinates.

Steepest Descents did not converge to Fmax < 1000 in 50001 steps.
Potential Energy  = -2.17266924593509e+05
Maximum force =  2.89751132744731e+04 on atom 8524
Norm of force =  2.18622026854678e+02

Thanks for any advice,

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Re: [gmx-users] How to examine the problem of one atom during EM

2011-07-27 Thread lina

On Wed, Jul 27, 2011 at 7:29 PM, Justin A. Lemkul  wrote:
>
>
> lina wrote:
>>
>> Hi,
>>
>> Form the begining to 5 steps, during EM, all exit in atom 8524,
>> how do I check it further? I mean, from which parts to examine?
>> I also switched to double version to run the EM.
>>
>
> Open your structure in a visualization program and look at what it might be
> clashing with

Thanks, I checked before.


>
> -Justin
>
>> 
>> Step=42296, Dmax= 2.9e-10 nm, Epot= -2.17267e+05 Fmax= 1.49514e+04, atom=
>> 8524
>> ...
>> Step=42313, Dmax= 2.0e-10 nm, Epot= -2.17267e+05 Fmax= 2.23506e+04, atom=
>> 8524
>> ...
>> Step=5, Dmax= 1.7e-10 nm, Epot= -2.17267e+05 Fmax= 2.89751e+04, atom=
>> 8524
>>
>> writing lowest energy coordinates.
>>
>> Steepest Descents did not converge to Fmax < 1000 in 50001 steps.
>> Potential Energy  = -2.17266924593509e+05
>> Maximum force     =  2.89751132744731e+04 on atom 8524
>> Norm of force     =  2.18622026854678e+02
>>
>> Thanks for any advice,
>>
>
> --
> 
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> 
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Re: [gmx-users] How to examine the problem of one atom during EM

2011-07-27 Thread lina

On Wed, Jul 27, 2011 at 9:06 PM, Justin A. Lemkul  wrote:
>
>
> lina wrote:
>>
>> On Wed, Jul 27, 2011 at 7:29 PM, Justin A. Lemkul  wrote:
>>>
>>> lina wrote:
>>>>
>>>> Hi,
>>>>
>>>> Form the begining to 5 steps, during EM, all exit in atom 8524,
>>>> how do I check it further? I mean, from which parts to examine?
>>>> I also switched to double version to run the EM.
>>>>
>>> Open your structure in a visualization program and look at what it might
>>> be
>>> clashing with
>>
>> Thanks, I checked before.
>>
>
> And what did you find?  What is the closest atom to the one with the maximal
> force?  Would its charge cause repulsion?  Is it so close that LJ overlap is
> causing a problem?  In this case, visualization of the problematic structure
> is the solution, you just have to take care to identify the source of the
> problem.  It certainly may not always be obvious.

Thanks, I guess I might make the system so compact.

Before in VMD it showed something weird, kind of broken bond, but in
PyMOL was fine.

Thanks again,

>
> -Justin
>
>>
>>> -Justin
>>>
>>>> 
>>>> Step=42296, Dmax= 2.9e-10 nm, Epot= -2.17267e+05 Fmax= 1.49514e+04,
>>>> atom=
>>>> 8524
>>>> ...
>>>> Step=42313, Dmax= 2.0e-10 nm, Epot= -2.17267e+05 Fmax= 2.23506e+04,
>>>> atom=
>>>> 8524
>>>> ...
>>>> Step=5, Dmax= 1.7e-10 nm, Epot= -2.17267e+05 Fmax= 2.89751e+04,
>>>> atom=
>>>> 8524
>>>>
>>>> writing lowest energy coordinates.
>>>>
>>>> Steepest Descents did not converge to Fmax < 1000 in 50001 steps.
>>>> Potential Energy  = -2.17266924593509e+05
>>>> Maximum force     =  2.89751132744731e+04 on atom 8524
>>>> Norm of force     =  2.18622026854678e+02
>>>>
>>>> Thanks for any advice,
>>>>
>>> --
>>> 
>>>
>>> Justin A. Lemkul
>>> Ph.D. Candidate
>>> ICTAS Doctoral Scholar
>>> MILES-IGERT Trainee
>>> Department of Biochemistry
>>> Virginia Tech
>>> Blacksburg, VA
>>> jalemkul[at]vt.edu | (540) 231-9080
>>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>>
>>> 
>>> --
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>>>
>>
>>
>>
>
> --
> ====
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> 
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Re: [gmx-users] bug in editconf for making a box ? combined two residues into one

2011-08-03 Thread lina

On Wed, Aug 3, 2011 at 9:13 PM, maria goranovic
 wrote:
> Hi
> I am using editconf to set my box to the right size using:
> editconf -f in.gro -o out.gro -box 30 30 30
> gromacs v. 4.5.3
> For this example, my system contains a phosphate anion and a water molecule.
> After editconf runs, it changes the residue name SOL of the water molecule
> to the residue name PHO for phosphate, because both have the same residue
> number (1). Is this not a bug, or am I doing something really silly? One can
> always try to run a simulation of an amino acid in water, and the error
> below would be replicated?
> Interestingly, grompp does not complain that the residue PHO has 8 atoms
> instead of 5 as in the topology file.
> I do not see this problem if the residue number of the water molecule is 2
> instead of 1.
> Below are the two .gro files, before and after running the above command.
>
> GROtesk MACabre and Sinister
> 8
>     1PHO    O1P    1  13.422   2.753   5.900
>     1PHO      P    2  13.250   2.818   5.976
>     1PHO    O2P    3  13.193   2.967   5.853
>     1PHO    O3P    4  13.263   2.864   6.169
>     1PHO    O4P    5  13.118   2.672   5.939
>     1SOL     OW    1  12.025   1.421  -1.203
>     1SOL    HW1    2  12.125   1.421  -1.203
>     1SOL    HW2    3  11.993   1.516  -1.203
> 20 20 20
>
> GROtesk MACabre and Sinister
>     8
>     1PHO    O1P    1  15.623  15.449  17.622
>     1PHO      P    2  15.451  15.514  17.697
>     1PHO    O2P    3  15.394  15.663  17.574
>     1PHO    O3P    4  15.464  15.560  17.890
>     1PHO    O4P    5  15.319  15.368  17.660
>     1PHO     OW    6  14.226  14.117  10.518
>     1PHO    HW1    7  14.326  14.117  10.518
>     1PHO    HW2    8  14.194  14.212  10.518
>   30.0  30.0  30.0
>
>

There is a problem in your in.gro.

try:

GROtesk MACabre and Sinister
8
1PHOO1P1  13.422   2.753   5.900
1PHO  P2  13.250   2.818   5.976
1PHOO2P3  13.193   2.967   5.853
1PHOO3P4  13.263   2.864   6.169
1PHOO4P5  13.118   2.672   5.939
2SOL OW6  12.025   1.421  -1.203
2SOLHW17  12.125   1.421  -1.203
2SOLHW28  11.993   1.516  -1.203
20 20 20

then there will be no problem.

>
>
> --
> Maria G.
> Technical University of Denmark
> Copenhagen
>
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Re: [gmx-users] Regarding Segmentation fault during mdrun_d

2011-08-04 Thread lina

On Thu, Aug 4, 2011 at 3:03 PM, Ravi Kumar Venkatraman
 wrote:
> Dear All,
>  I was trying to run NVT equilibration for cyclohexane. When I
> started running it shows following error
>
> Reading file nvt.tpr, VERSION 4.5.4 (double precision)
> Starting 2 threads
> Making 1D domain decomposition 2 x 1 x 1
> starting mdrun 'Cyclohexane box'
> 5 steps,    100.0 ps.
> Segmentation fault.
>
> Please suggest me something to overcome this.
>
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try mdrun -pd

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Re: [gmx-users] How to run solvation dynamics for some organic molecules

2011-08-05 Thread lina

On Fri, Aug 5, 2011 at 7:23 PM, Ravi Kumar Venkatraman
 wrote:
> Dear all,
>  I have generated .gro and .top file for Chloranil from prodrg
> and tried solvate it using pre-equilibrated cyclohexane. When i tried to
> generate the box containing solute it is not modifying the .top file and it
> shows zero solvent.
> Please help me how to solvate organic molecules that are obtainde from
> prodrg.
>
> Thank you.


Try:

genbox -cp chloranil.gro -cs cyclohexane.gro -o system.gro


and manually modify the topol.top later.

you may use the solvated pre-equilibrated cyclohexane as
cyclohexane.gro, so no need add water later.

It should be no problem.
>
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[gmx-users] how to calculate the conc in the genion

2011-08-11 Thread lina

Hi,

after using genion -conc 0.1

certain number of Na and Cl were added in solvent.

but when I tried to calculate back, namely, based on the number of Na
and Cl, the number of water molecular and the box volumn,
but seems can't come back, I mean, can't obtain the result of 0.1mol/L.

I read the manual, "...the specified concentration as computed from
the volume of the cell..."

the cell? Has anyone tried to calculate the concentration back?

( I guess might the way I calculate was wrong? the Avogadro's Constant
= 6.0221415 × 10^23 mol-1)


Thanks with best regards,

lina
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Re: [gmx-users] How to install gromacs 4.5.1

2011-08-11 Thread lina

cd /usr/lib

(or locate libfftw3.so.3.2.4)

you may notice the /usr/lib/libfftw3.so.3.2.4

make a link,
sudo ln -sf /usr/lib/libfftw3.so.3.2.4 /usr/lib/libfftw3.so.3

then shall be no problem.


On Thu, Aug 11, 2011 at 10:50 PM, Mark Abraham  wrote:
> On 12/08/2011 12:38 AM, afsaneh maleki wrote:
>
> Hi,
>
> My characteristics computer:
>
>
>
> Root at …fftw-3.2.2]# uname -a
>
> Linux localhost.localdomain 2.6.31.5-127.fc12.i686.PAE #1 SMP Sat Nov 7
> 21:25:57 EST 2009 i686 i686 i386 GNU/Linux
>
>
>
> To install FFTW version 3.2.2.
>
> I used the following commands:
>
> Root at …fftw-3.2.2]#  ./configure --enable-threads --enable-float
> --enable-shared
>
>   Root at …fftw-3.2.2]#  make
>
>   Root at …fftw-3.2.2]#  make install
>
> After using “make” and “make install”, it get me the following text at end:
>
> make[3]: Leaving directory `/home/afsaneh/m/fftw-3.2.2/tools'
>
> make[2]: Leaving directory `/home/afsaneh/m/fftw-3.2.2/tools'
>
> Making all in m4
>
> make[2]: Entering directory `/home/afsaneh/m/fftw-3.2.2/m4'
>
> make[2]: Nothing to be done for `all'.
>
> make[2]: Leaving directory `/home/afsaneh/m/fftw-3.2.2/m4'
>
> make[1]: Leaving directory `/home/afsaneh/m/fftw-3.2.2'
>
>
>
> ..
>
> To install gromacs version 4.5.1
>
> root@localhost gromacs-4.5.1]#./configure
>
> You aren't configuring to use fftw3. You should probably use the same
> --enable-shared setting for both FFTW and GROMACS.
>
> * On most platforms you can save 10X space with dynamic libraries, although
>
>   the binaries might be less portable. Why not try --enable-shared ?
>
>
>
> [root@localhost gromacs-4.5.1]#make
>
> [root@localhost gromacs-4.5.1]#make install
>
> [root@localhost gromacs-4.5.1]# make links
>
> cd /usr/local/gromacs/bin && programs=`ls` && cd /usr/local/bin && \
>
>     for i in $programs; do \
>
>        (test ! -f $i && ln -s /usr/local/gromacs/bin/$i . ; exit 0);
> \
>
>     done
>
>
>
> when i used each command with” –h” or “–help” I obtain the followinf error:
>
> [afsaneh@localhost ~]$ g_analyze -h
>
> g_analyze: error while loading shared libraries: libfftw3f.so.3: cannot open
> shared object file: No such file or directory
>
> Sounds like somehow the make environment could find the FFTW libraries, but
> the execution environment could not. Do heed the advice here
> http://www.gromacs.org/Downloads/Installation_Instructions#Getting_access_to_GROMACS_after_installation
> (and the rest of the instructions, too)
>
> Mark
>
>
>
> [afsaneh@localhost ~]$ editconf -h
>
> editconf: error while loading shared libraries: libfftw3f.so.3: cannot open
> shared object file: No such file or directory
>
>
>
> How to solve this problem?
>
>
>
> Best wishes,
>
> Afsaneh
>
>
>
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>



-- 
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lina
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Re: [gmx-users] how to calculate the conc in the genion

2011-08-11 Thread lina

On Thu, Aug 11, 2011 at 10:41 PM, Mark Abraham  wrote:
> On 12/08/2011 12:37 AM, lina wrote:
>>
>> Hi,
>>
>> after using genion -conc 0.1
>>
>> certain number of Na and Cl were added in solvent.
>>
>> but when I tried to calculate back, namely, based on the number of Na
>> and Cl, the number of water molecular and the box volumn,
>> but seems can't come back, I mean, can't obtain the result of 0.1mol/L.
>>
>> I read the manual, "...the specified concentration as computed from
>> the volume of the cell..."
>>
>> the cell? Has anyone tried to calculate the concentration back?
>>
>> ( I guess might the way I calculate was wrong? the Avogadro's Constant
>> = 6.0221415 в 10^23 mol-1)
>
> I'd be amazed if the error was in the code and not in your calculation. The
> number of water molecules doesn't matter for the calculation of the ion
> concentration, of course. Pay attention to your box shape. And do consider
> the number of ions has to be an integer, so for a given volume you cannot
> get arbitrarily close to a given concentration.

I did use the box volumn first, but a bit far away from it.

so I wonder whether it means the concentration of the solvent involved,

another concern, what if the cell has large area no water, so how the
concentration calculated, still the whole box?

Thanks,
>
> Mark
> --
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-- 
Best Regards,

lina
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Re: [gmx-users] how to calculate the conc in the genion

2011-08-11 Thread lina

On Thu, Aug 11, 2011 at 11:35 PM, Tsjerk Wassenaar  wrote:
> Hi,
>
>>> I'd be amazed if the error was in the code and not in your calculation. The
>>> number of water molecules doesn't matter for the calculation of the ion
>>> concentration, of course. Pay attention to your box shape. And do consider
>>> the number of ions has to be an integer, so for a given volume you cannot
>>> get arbitrarily close to a given concentration.
>
> The error is, to my humble opinion, in the reasoning. Concentration is
> a macroscopic property, and when dealing with a minute volume, the
> concentration of something in it is ill defined. Especially when
> there's something else in that volume, taking up a significant amount
> of space, like a membrane, protein or void, it becomes troublesome. I
> would argue that the worst you can do in that case is take the volume
> of the box and calculate the number of things to add from there to
> reach a given concentration.
> Whether the number of water molecules matters for the calculation of
> the ion concentration depends on the unit you use for concentration.
> Probably  molality is a better option than molarity. For that you do
> take the number of water molecules. Frankly, that's what I usually do.
> Doing so will give a desired concentration of ions in the solvent,
> regardless of volume occupied by other (big) solutes or by nothing.
> There is just one problem that stays nonetheless; in how far does the
> bulk concentration you use as target correspond to the local
> concentration you might need to use? Solutes, membranes and voids may
> alter the local concentration significantly.
>
> By the way, Lina, it would have helped if you had given the equations,
> numbers and outcomes that lead you to believe there is something
> wrong.

I did another quick check, which regardless of my way of calculation.

two cubic box, the same conc.
I compared the ratio of  Na+CL in two box  is 24/60=0.4
while I compared the volumn ratio is 149.6/533.39=0.28.

This way is easily for others to check too. read the ions from two
topol.top and the dimension from two .gro.

>
> Hope it helps,

Thanks,
>
> Tsjerk
>
>
>
> --
> Tsjerk A. Wassenaar, Ph.D.
>
> post-doctoral researcher
> Molecular Dynamics Group
> * Groningen Institute for Biomolecular Research and Biotechnology
> * Zernike Institute for Advanced Materials
> University of Groningen
> The Netherlands
> --
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>



-- 
Best Regards,

lina
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Re: [gmx-users] how to calculate the conc in the genion

2011-08-11 Thread lina

On Thu, Aug 11, 2011 at 11:35 PM, Tsjerk Wassenaar  wrote:
> Hi,
>
>>> I'd be amazed if the error was in the code and not in your calculation. The
>>> number of water molecules doesn't matter for the calculation of the ion
>>> concentration, of course. Pay attention to your box shape. And do consider
>>> the number of ions has to be an integer, so for a given volume you cannot
>>> get arbitrarily close to a given concentration.
>
> The error is, to my humble opinion, in the reasoning. Concentration is
> a macroscopic property, and when dealing with a minute volume, the
> concentration of something in it is ill defined. Especially when
> there's something else in that volume, taking up a significant amount
> of space, like a membrane, protein or void, it becomes troublesome. I
> would argue that the worst you can do in that case is take the volume
> of the box and calculate the number of things to add from there to
> reach a given concentration.
> Whether the number of water molecules matters for the calculation of
> the ion concentration depends on the unit you use for concentration.
> Probably  molality is a better option than molarity. For that you do
> take the number of water molecules. Frankly, that's what I usually do.
> Doing so will give a desired concentration of ions in the solvent,
> regardless of volume occupied by other (big) solutes or by nothing.
> There is just one problem that stays nonetheless; in how far does the
> bulk concentration you use as target correspond to the local
> concentration you might need to use? Solutes, membranes and voids may
> alter the local concentration significantly.
>

Yes. I do agree with you.

Here I have a field problem, I will be very glad if I can be told
which part of calculation is wrong.

a cubic box: Volumn = 101.57 *105.03 * 87.82 A  = 9.369E-25  m^3 = 93.69E-23 L
total ions: 121

so the concentration based on the box volume is:

121/AvagadroConstant/Volumn =
121/6.022E23/93.69E-23=121/6.022/9.369=0.214 mol/L?

But before when I used -conc, the number I chose maybe 0.1 or 0.15
mol/L, but not 0.2mol/L.

Here if consider the water, certainly the water volumn will be greatly
smaller than the box volumn, so the concentration will reach very
high?

I might be wrong in some way, hope someone can point out.

Thanks,

> By the way, Lina, it would have helped if you had given the equations,
> numbers and outcomes that lead you to believe there is something
> wrong.
>
> Hope it helps,
>
> Tsjerk
>
>
>
> --
> Tsjerk A. Wassenaar, Ph.D.
>
> post-doctoral researcher
> Molecular Dynamics Group
> * Groningen Institute for Biomolecular Research and Biotechnology
> * Zernike Institute for Advanced Materials
> University of Groningen
> The Netherlands
> --
> gmx-users mailing list    gmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
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> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
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> www interface or send it to gmx-users-requ...@gromacs.org.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>



-- 
Best Regards,

lina
--
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Re: [gmx-users] how to calculate the conc in the genion

2011-08-11 Thread lina

On Fri, Aug 12, 2011 at 8:08 AM, Mark Abraham  wrote:
> On 12/08/2011 2:22 AM, lina wrote:
>>
>> On Thu, Aug 11, 2011 at 11:35 PM, Tsjerk Wassenaar
>>  wrote:
>>>
>>> Hi,
>>>
>>>>> I'd be amazed if the error was in the code and not in your calculation.
>>>>> The
>>>>> number of water molecules doesn't matter for the calculation of the ion
>>>>> concentration, of course. Pay attention to your box shape. And do
>>>>> consider
>>>>> the number of ions has to be an integer, so for a given volume you
>>>>> cannot
>>>>> get arbitrarily close to a given concentration.
>>>
>>> The error is, to my humble opinion, in the reasoning. Concentration is
>>> a macroscopic property, and when dealing with a minute volume, the
>>> concentration of something in it is ill defined. Especially when
>>> there's something else in that volume, taking up a significant amount
>>> of space, like a membrane, protein or void, it becomes troublesome. I
>>> would argue that the worst you can do in that case is take the volume
>>> of the box and calculate the number of things to add from there to
>>> reach a given concentration.
>>> Whether the number of water molecules matters for the calculation of
>>> the ion concentration depends on the unit you use for concentration.
>>> Probably  molality is a better option than molarity. For that you do
>>> take the number of water molecules. Frankly, that's what I usually do.
>>> Doing so will give a desired concentration of ions in the solvent,
>>> regardless of volume occupied by other (big) solutes or by nothing.
>>> There is just one problem that stays nonetheless; in how far does the
>>> bulk concentration you use as target correspond to the local
>>> concentration you might need to use? Solutes, membranes and voids may
>>> alter the local concentration significantly.
>>>
>> Yes. I do agree with you.
>>
>> Here I have a field problem, I will be very glad if I can be told
>> which part of calculation is wrong.
>>
>> a cubic box: Volumn = 101.57 *105.03 * 87.82 A  = 9.369E-25  m^3 =
>> 93.69E-23 L
>> total ions: 121
>>
>> so the concentration based on the box volume is:
>>
>> 121/AvagadroConstant/Volumn =
>> 121/6.022E23/93.69E-23=121/6.022/9.369=0.214 mol/L?
>>
>> But before when I used -conc, the number I chose maybe 0.1 or 0.15
>> mol/L, but not 0.2mol/L.
>
> That's the concentration of total ions, but the concentration of each ionic
> species is about half that.

Thanks, I should not have used total number of ions.


>
> Mark
>
>>
>> Here if consider the water, certainly the water volumn will be greatly
>> smaller than the box volumn, so the concentration will reach very
>> high?
>>
>> I might be wrong in some way, hope someone can point out.
>>
>> Thanks,
>>
>>> By the way, Lina, it would have helped if you had given the equations,
>>> numbers and outcomes that lead you to believe there is something
>>> wrong.
>>>
>>> Hope it helps,
>>>
>>> Tsjerk
>>>
>>>
>>>
>>> --
>>> Tsjerk A. Wassenaar, Ph.D.
>>>
>>> post-doctoral researcher
>>> Molecular Dynamics Group
>>> * Groningen Institute for Biomolecular Research and Biotechnology
>>> * Zernike Institute for Advanced Materials
>>> University of Groningen
>>> The Netherlands
>>> --
>>> gmx-users mailing list    gmx-users@gromacs.org
>>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>>> Please search the archive at
>>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>>> Please don't post (un)subscribe requests to the list. Use the
>>> www interface or send it to gmx-users-requ...@gromacs.org.
>>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>>
>>
>>
>
> --
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> http://lists.gromacs.org/mailman/listinfo/gmx-users
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-- 
Best Regards,

lina
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Re: [gmx-users] mdrun crashes with 'One or more interactions were multiple assigned in the domain decompostion'

2011-08-12 Thread lina

On Fri, Aug 12, 2011 at 7:55 PM, Sebastian Breuers
 wrote:
> Dear all,
>
> searching for the mentioned error message I found a bug report for mdrun. It
> seemed to be fixed, but in my setup it appears again and I am not sure if I
> could do something about it.
>
> I did not attach the tpr file since it is bounced by the mailing list and
> I'd like to get at least a hint without waitng for approval of the rejected
> mail. :)
> The simulation crashes with 64 CPUs after step 11237000 with the following
> entry in the log file:
>
> ---
> Program mdrun, VERSION 4.5.4
> Source code file:
> /home/breuerss/local/src/gromacs-4.5.4/src/mdlib/domdec_top.c, line: 352
>
> Software inconsistency error:
> One or more interactions were multiple assigned in the domain decompostion
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> ---
>
> That means that the simulation already ran for some time. I could also
> finish some runs successfully with the very same topology but different
> simulation parameters.
>
> For any help or hints how I could fix it I would be grateful.

Have you tried to re-submit it, use the -cpi state.cpt -append

and see whether it can continue or not?

>
> Best regards
>
>
> Sebastian
>
> --
> _
>
> Sebastian Breuers               Tel: +49-221-470-4108
> EMail: breue...@uni-koeln.de
>
> Universität zu Köln             University of Cologne
> Department für Chemie           Department of Chemistry
> Organische Chemie               Organic Chemistry
>
> Greinstraße 4                   Greinstraße 4
> Raum 325                        Room 325
> D-50939 Köln                    D-50939 Cologne, Federal Rep. of Germany
> _
>
> --
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> http://lists.gromacs.org/mailman/listinfo/gmx-users
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-- 
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lina
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Re: [gmx-users] Regarding g_sham

2011-08-13 Thread lina

On Sat, Aug 13, 2011 at 3:36 PM, bipin singh  wrote:
> Hello,
> Please let me know from where can I get the full description of g_sham
> module, as the manual does not
> provide full description of the options for g_sham in gromacs.
> for e.g I want to know the description about the following options in g_sham:
>
> -map
> -ls3
> -mdata
>

Sorry, I am not sure what's kind of "full description" you expect,

Try:

g_sham -h

or

man g_sham

>
>
> --
> ---
> Regards,
> Bipin Singh
> --
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lina
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Re: [gmx-users] termini modification

2011-08-27 Thread lina

pdb2gmx -ter

On Sat, Aug 27, 2011 at 6:17 PM, Vijayaraj  wrote:
> Hello,
>
> I am using gromacs 4.5.4 with amber99sb ff. I would like to modify the
> terminal residues from NALA and CALA to normal ALA (just as middle
> residues). As the terminal selection option is not enabled with the amber
> ff, I am using the termini modification parameters with aminoacids.c.tdb.
> here is my code for the aminoacids.c.tdb
>
> [ COO- ]
>
> [ replace ]
> H    H    1.00800        0.27190
> N    N    14.01000    -0.41570
> CA    CT    12.01000    0.03370
> HA    H1    1.00800        0.08230
> C    C    12.01000    0.59730
> CB    CT    12.01        -0.1825
> HB1    HC    1.008        0.0603
> HB2    HC    1.008        0.0603
> HB3    HC    1.008        0.0603
>
> [ add ]
> 1    1    O    C    CA    N
>         O    16.0    -0.56790
>
> [ bonds ]
> C    O     1    0.12290        476976.0
>
> [ delete ]
> OC1
> OC2
>
>
> when I run pdb2gmx using this termini modification, everything works fine
> except the deletion of OC1 and OC2 atoms, the error which I get for this run
> as follows,
>
> Fatal error:
> Atom OC2 not found in residue seq.nr. 8 while adding atom
>
>
> any suggestion to delete the OC1 and OC2 atoms. If I dont enable this [
> delete ] option with the aminoacids.c.tdb file, it works fine by adding the
> O atom to the terminal residue including the presence of OC1 and OC2 atoms.
> first I am trying to modify the c terminal residue.
>
> Regards,
> vijay.
>
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Re: [gmx-users] no output in g_dist

2011-09-08 Thread lina

On Thu, Sep 8, 2011 at 8:25 PM, aiswarya pawar  wrote:
> Hi users,
>
> To get the distance between water and protein i did -
>
>  g_dist -f md.xtc -s md.tpr -o distance.xvg -dist 1 -b 1 -e 11
>
> from this i should obtain an output file as distance.xvg which i dont get.

The -dist option: Print all atoms in group 2 (water) closer than dist to
the center of mass of group 1 (protein in
your case).

As you have seen, it *print* the result on the screen.

To obtain the distance.xvg file, please don't use the -dist option here.

>
> and my output is printed on the terminal as-
>
> t: 1  136 SOL 2336 OW  0.772373 (nm)
> t: 1  136 SOL 2337 HW1  0.706358 (nm)
> t: 1  136 SOL 2338 HW2  0.807787 (nm)
> t: 1  139 SOL 2345 OW  0.821094 (nm)
> t: 1  139 SOL 2346 HW1  0.810919 (nm)
> t: 1  139 SOL 2347 HW2  0.771526 (nm)
> t: 1  7237 SOL 23640 HW1  0.997056 (nm)
> t: 1  11793 SOL 37307 OW  0.868929 (nm)
> t: 1  11793 SOL 37308 HW1  0.927205 (nm)
> t: 1  11793 SOL 37309 HW2  0.776699 (nm)
> t: 2  125 SOL 2303 OW  0.940527 (nm)
>
> In this
>
> t: 1  136 SOL 2336 OW  0.772373 (nm)
>
> does the 't' states the time frame, 136 SOL states the SOL molecule number
> and 2336 OW the residue contact from protein and the 0.772373 nm the
> distance between them.
>
> Thanks
>
>
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[gmx-users] md.mdp file GPU one

2011-09-09 Thread lina

Hi,


are there someone love to share one md.mdp file for GPU version?


Thanks ahead,

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Re: [gmx-users] md.mdp file GPU one

2011-09-09 Thread lina

On Fri, Sep 9, 2011 at 8:48 PM, Justin A. Lemkul  wrote:

>
>
> lina wrote:
>
>> Hi,
>>
>>
>> are there someone love to share one md.mdp file for GPU version?
>>
>>
> All the details are here:
>
> http://www.gromacs.org/**Downloads/Installation_**
> Instructions/GPUs?highlight=**gpu<http://www.gromacs.org/Downloads/Installation_Instructions/GPUs?highlight=gpu>
>
> The benchmark archive has example .mdp files that you can tweak.
>

Thanks. ( From those warnings, started to realize its limitations, no plan
to try further recently. ^_^ )


>
> -Justin
>
> --
> ==**==
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
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>
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Re: [gmx-users] radial distribution function

2011-09-09 Thread lina

On Sat, Sep 10, 2011 at 3:35 AM, Moeed  wrote:

> Dear users,
>
> I have created radial distribution function plot for Carbon atoms in a
> system containing polymer chains. I see some little jumps between first and
> second peak.
> I need your help to comment on how this behavior can be justified (or if
> the plot is wrong).
>
> g_rdf -f *.trr -s *.tpr -o *.xvg -n *.ndx –b xxx
> Thank you in advance.
>

I think your figure is fine.

You just need how to proper interpret your figures, truly understand what
the "radial distribution" means.


>
>
>
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[gmx-users] how to modify the md. log

2011-09-10 Thread lina

Hi,

My job terminated due to the storage out of the quote given by
administrator,

here the md.log is unusual, so when I resume the job, the results won't
append on it. but still running...

Here is the tail of md.log,

DD  step 31424999 load imb.: force 20.8%  pme mesh/force 1.936

   Step   Time Lambda
   3142500062850.00.0

<...snip...>

DD  step 31425999 load imb.: force 23.7%  pme mesh/force 1.923

   Step   Time Lambda
   3142600062852.00.0

<...snip...>
Kinetic En.   Total EnergyTemperature [lina@hostname


You may notice that the [lina@hostname] did not start in a new line.

there is md_step31441735.cpt
and md_prev.cpt

what is the final step stored in the md_prev.cpt? How do I check ?

are there some chance to resume?

Thanks ahead,

Best regards,

lina
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[gmx-users] Re: how to modify the md. log

2011-09-10 Thread lina

On Sat, Sep 10, 2011 at 5:05 PM, lina  wrote:

> Hi,
>
> My job terminated due to the storage out of the quote given by
> administrator,
>
> here the md.log is unusual, so when I resume the job, the results won't
> append on it. but still running...
>
> Here is the tail of md.log,
>
> DD  step 31424999 load imb.: force 20.8%  pme mesh/force 1.936
>
>Step   Time Lambda
>3142500062850.00.0
>
> <...snip...>
>
> DD  step 31425999 load imb.: force 23.7%  pme mesh/force 1.923
>
>Step   Time Lambda
>3142600062852.00.00000
>
> <...snip...>
> Kinetic En.   Total EnergyTemperature [lina@hostname
>
>
> You may notice that the [lina@hostname] did not start in a new line.
>
> there is md_step31441735.cpt
> and md_prev.cpt
>
> what is the final step stored in the md_prev.cpt? How do I check ?
>

gmxcheck shows:

Last frame -1 time 62400.328

End of file on md.xtc but not on md_prev.cpt

Thanks,



>
>
>
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Re: [gmx-users] radial distribution function

2011-09-10 Thread lina

On Sat, Sep 10, 2011 at 10:00 PM, Moeed  wrote:

> Thank you for your input. I am going to run for another 15 ns to see if the
> little jumps vanish.
>
> Best,
>
> g_rdf -bin
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Re: [gmx-users] how to modify the md. log

2011-09-10 Thread lina

On Sat, Sep 10, 2011 at 8:45 PM, Justin A. Lemkul  wrote:

>
>
> lina wrote:
>
>> Hi,
>>
>> My job terminated due to the storage out of the quote given by
>> administrator,
>>
>> here the md.log is unusual, so when I resume the job, the results won't
>> append on it. but still running...
>>
>> Here is the tail of md.log,
>>
>>DD  step 31424999  load imb.: force 20.8%  pme
>> mesh/force 1.936
>>
>>   Step   Time Lambda
>>   31425000 62850.00.0
>>
>> <...snip...>
>>
>> DD  step 31425999  load imb.: force 23.7%  pme mesh/force
>> 1.923
>>
>>   Step   Time Lambda
>>   31426000 62852.00.0
>>
>>
>> <...snip...>
>>Kinetic En.   Total EnergyTemperature [lina@hostname
>>
>>
>> You may notice that the [lina@hostname] did not start in a new line.
>>
>> there is md_step31441735.cpt
>> and md_prev.cpt
>>
>> what is the final step stored in the md_prev.cpt? How do I check ?
>>
>>
> It should be the step -cpt minutes before the later checkpoint was written.
>  Use gmxcheck to verify its contents.
>
>
>  are there some chance to resume?
>>
>>
> Make sure the existing job has been killed (which sounds like it may or may
> not be the case) and simply restart from the appropriate checkpoint.
>
> http://www.gromacs.org/**Documentation/How-tos/Doing_**Restarts<http://www.gromacs.org/Documentation/How-tos/Doing_Restarts>
>
> -Justin
>

Thanks.


>
> --
> ==**==
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>
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[gmx-users] How do I examine the results didn't write issue

2011-09-12 Thread lina

Hi,

I am confused, why the job is running,

but they did not write the .edr, .log .xtc ... files.

Everything showed so normal, just not writing,

when I used thread, all is fine, the writing is normal.

just use mpi, I tried different nodes, still not work, now two hours later,
still no writing, just running.

Thanks for providing any clue for me to examine.


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Re: [gmx-users] How do I examine the results didn't write issue

2011-09-12 Thread lina

On Mon, Sep 12, 2011 at 8:33 PM, Justin A. Lemkul  wrote:

>
>
> lina wrote:
>
>> Hi,
>>
>> I am confused, why the job is running,
>>
>> but they did not write the .edr, .log .xtc ... files.
>>
>> Everything showed so normal, just not writing,
>>
>> when I used thread, all is fine, the writing is normal.
>>
>> just use mpi, I tried different nodes, still not work, now two hours
>> later, still no writing, just running.
>>
>> Thanks for providing any clue for me to examine.
>>
>>
>>
> Sounds like your MPI implementation is broken or you haven't issued the
> command right.  If you have a test command that you know should work, run
> that. Otherwise, it's impossible to know if the problem is with Gromacs or
> something external.  If you compiled with threading support, but not MPI (in
> a separate binary) then MPI will not work on the thread-enabled executable.
>

I suspected it's MPI issue, but couple of days ago it's fine, and the
results was able to write.

I installed both MPI and thread but with different prefix to distinguish.

Thanks,

>
> -Justin
>
> --
> ==**==
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>
> ==**==
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Re: [gmx-users] How do I examine the results didn't write issue

2011-09-12 Thread lina

On Mon, Sep 12, 2011 at 8:35 PM, Mark Abraham wrote:

> On 12/09/2011 10:23 PM, lina wrote:
>
>> Hi,
>>
>> I am confused, why the job is running,
>>
>> but they did not write the .edr, .log .xtc ... files.
>>
>> Everything showed so normal, just not writing,
>>
>> when I used thread, all is fine, the writing is normal.
>>
>> just use mpi, I tried different nodes, still not work, now two hours
>> later, still no writing, just running.
>>
>
> If you can run mdrun_threads -np 4 and get output and your mpirun -np 4
> mdrun_mpi does not write output, then there must be something wrong with
> your MPI environment. Try another MPI program and see what it does.
>

I guess I will drop an email to the administrator.

might be an MPI issue.

Thanks for your time,


> Mark
>
> --
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[gmx-users] about non-writing issue

2011-09-18 Thread lina

Hi,

Very sporadically and also with high frequent,

The job I submitted only running without writing (this job is not un-started
one, mainly one I stopped and rerun).

Before I thought I did not wait long enough, such as hours, but seriously
after 3 or 8 hours, still running not writing.

I ssh to each nodes, all is fully running.

The storage is NFS, I/O flow can't be choked for hours.

Really headache, sometimes it works.

I have had no clue about it.


Thanks for any suggestions,


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[gmx-users] Re: about non-writing issue

2011-09-18 Thread lina

Hi,

It works now.

Not write (just based on guess) might
the md.log step such as is 1114
while use thread I noticed the actually run step started from 11135000

so I run until it can write to the md.log

then switch to 1 node to run for a while,

then switch to more nodes.

But there might be some reason there which I don't know.

Thanks,

On Sun, Sep 18, 2011 at 4:35 PM, lina  wrote:

> Hi,
>
> Very sporadically and also with high frequent,
>
> The job I submitted only running without writing (this job is not
> un-started one, mainly one I stopped and rerun).
>
> Before I thought I did not wait long enough, such as hours, but seriously
> after 3 or 8 hours, still running not writing.
>
> I ssh to each nodes, all is fully running.
>
> The storage is NFS, I/O flow can't be choked for hours.
>
> Really headache, sometimes it works.
>
> I have had no clue about it.
>
>
> Thanks for any suggestions,
>
>
> --
> Best Regards,
>
> lina
>
>
>


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Re: [gmx-users] Re: about non-writing issue

2011-09-18 Thread lina

On Mon, Sep 19, 2011 at 11:31 AM, Jianguo Li  wrote:

> I met the similar problem before, sometimes my job writes output, sometimes
> not. My cluster administrator fixed the problem and they told me that there 
> were
> some problem at some compute nodes which my job unfortunately was dispatched
> to.
>

Last time I contacted the administrator, he told me it's due to the
restriction he set, I mean, I could only use limited nodes.
He loosed the configuration a bit and it worked at that time.

But later it has happened, I don't have convincing confidence to email root
again.
So just try to figure out slowly.

Thanks for your answering,


>
> Jianguo
>
>
> --
> *From:* lina 
> *To:* Discussion list for GROMACS users 
> *Sent:* Sunday, 18 September 2011 5:13 PM
> *Subject:* [gmx-users] Re: about non-writing issue
>
> Hi,
>
> It works now.
>
> Not write (just based on guess) might
> the md.log step such as is 1114
> while use thread I noticed the actually run step started from 11135000
>
> so I run until it can write to the md.log
>
> then switch to 1 node to run for a while,
>
> then switch to more nodes.
>
> But there might be some reason there which I don't know.
>
> Thanks,
>
> On Sun, Sep 18, 2011 at 4:35 PM, lina  wrote:
>
> Hi,
>
> Very sporadically and also with high frequent,
>
> The job I submitted only running without writing (this job is not
> un-started one, mainly one I stopped and rerun).
>
> Before I thought I did not wait long enough, such as hours, but seriously
> after 3 or 8 hours, still running not writing.
>
> I ssh to each nodes, all is fully running.
>
> The storage is NFS, I/O flow can't be choked for hours.
>
> Really headache, sometimes it works.
>
> I have had no clue about it.
>
>
> Thanks for any suggestions,
>
>
> --
> Best Regards,
>
> lina
>
>
>
>
>
> --
> Best Regards,
>
> lina
>
>
>
> --
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-- 
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lina
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Re: [gmx-users] MD with membrane protein

2011-09-21 Thread lina

On Thu, Sep 22, 2011 at 11:34 AM, elisa carli wrote:

> Dear All
>
> I'd like to perfom a MD simulation on a membrane protein using DLPC or DPPC
> system
> I've downloaded the API package from this link
> http://www.gromacs.org/Downloads/User_contributions/Molecule_topologies
>
> DPPC.zip and DLPC.zip by schiu
>
> How can I use them? Where can I get a tutorial or commands illustrating the
> use of these packages?
>
> Thanks in advance
>
 Here is a rough procedure:

http://www.nanoconductor.org/43A1-S3/

Took Chiu's  DPPC.zip as an example. We use the speptide.pdb peptide from
the gromacs tutorial (it's a bad choice to put it in the dppc, but we just
try it).

pdb2gmx_g -f speptide.pdb -o speptide.gro

choose
9: GROMOS96 43a1 force field
1: SPCsimple point charge, recommended

$ tail -1 dppc.gro
   5.68585   5.60685   6.85739

To be as simple as possible here, we use the dimension of the dppc.gro

editconf_g -f speptide.gro -o speptide_newbox.gro -center 2.5 2.5 4.2  -box
5.68585   5.60685   6.85739

now solvate the peptide into the pre-equilibrillium-ed DPPC.gro by

genbox_g -cp speptide_newbox.gro -cs dppc.gro -o system.gro -p topol.top

Now cp the em.mdp from some_path_to/share/gromacs/tutor/speptide,

the purpose of doing a simple energy minimization here just want to "test"
the topol.top.

it used 43A1-S3 force field (You can download from
http://www.nanoconductor.org/43A1-S3/).

The head of topol.top:
; Include forcefield parameters
#include "ffG43A1-S3.itp"
#include "lipids_43A1-S3.itp"

The tail of topol.top:

[ molecules ]
; Compound#mols
Protein 1
DPPC 71
SOL  3205

I manually added DPPC  71.

please copy the  lipids_43A1-S3.itpffG43A1-S3.itp
ffG43A1-S3par.02.itp from the downloaded 43A1-S3 force field into current
directory,
extra copy ff_dum.itp from
some_path_to/share/gromacs/top/43a1s3.ff/ff_dum.itp into current working
directory.

I attached all those files in try.tar.gz
https://docs.google.com/leaf?id=0B93SVRfpVVg3ZmUxM2ExOTctYTJlNC00MzAxLWI4ZWItNDI2MGM4OThmN2Nj&hl=en_GB

mdrun_g -v -deffnm em

works well.

-- 
Best Regards,

lina
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Re: [gmx-users] error while install GMX4.5.5

2011-09-22 Thread lina

On Thu, Sep 22, 2011 at 8:11 PM, zhongjin  wrote:

> The system is Rocks 4.3 (Mars Hill), and
> [hzj1000@ZhouGroup ~]$ rpm -aq |grep glibc
> glibc-kernheaders-2.4-9.1.100.EL
> glibc-2.3.4-2.36
> glibc-headers-2.3.4-2.36
> glibc-common-2.3.4-2.36
> glibc-devel-2.3.4-2.36
>
> [hzj1000@ZhouGroup ~]$ gcc -v
> Reading specs from /usr/lib/gcc/i386-redhat-linux/3.4.6/specs
> Configured with: ../configure --prefix=/usr --mandir=/usr/share/man
> --infodir=/usr/share/info --enable-shared --enable-threads=posix
> --disable-checking --with-system-zlib --enable-__cxa_atexit
> --disable-libunwind-exceptions --enable-java-awt=gtk
> --host=i386-redhat-linux
> Thread model: posix
> gcc version 3.4.6 20060404 (Red Hat 3.4.6-8)
>
>
My gcc version is 4.6.1

probably it's nothing to do with your problem.

just probably you may wanna to undate your gcc.


> --
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-- 
Best Regards,

lina
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Re: [gmx-users] diferent version of gcc

2011-09-22 Thread lina

2011/9/23 Víctor Bahamonde 

>  Hello gmx users
>
> I have a question related to gromacs compilation
> in the  same machine, are there any difference in the result of MD when I
> compile the same version of gromacs but with diferent version of gcc?
> also, gcc 4.1.x still broken?
> I use Debian 5 and Debian 6 on amd phenom II quad core.
>
>
http://packages.debian.org/sid/gromacs
http://packages.debian.org/wheezy/gromacs

They have had already well built .deb ball there.
Install from your favoriate package management.


Thanks in advance.
>
> *Víctor E. Bahamonde Padilla
> Laboratorio de Fisicoquímica Molecular
> Departamento de Química
> Facultad de Ciencias
> Universidad de Chile
> Phone: 562-978-7443
> vedua...@ug.uchile.cl*
>
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-- 
Best Regards,

lina
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Re: [gmx-users] concentration distribution

2011-09-24 Thread lina

On Sep 25, 2011, at 0:33, raj  wrote:

> Hello,
> 
> I would like to calculate the concentration distribution of atoms along the x 
> and y axis from the trajectory. Can anybody suggest me a tool to calculate 
> this?

g_rdf ?!

> 
> regards,
> Raj
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Re: [gmx-users] MD with membrane protein

2011-10-03 Thread lina

On Tue, Oct 4, 2011 at 2:57 AM, elisa carli  wrote:

> Hi Lisa
>
Thank you very much for your reply.
> After minimimization could I run a molecular dynamic production?
> Or have I to do other sets?
>
Yes, after energy minimization, you need do some other sets (like NVT and
NPT).

Could you write me which are the commands to execute up to MD run?
>

The links Justin provided are very useful. It's not a bad idea to do some
tutor to be familiar with those procedures.


>
> Bests
>
> 2011/9/22 lina 
>
>>  On Thu, Sep 22, 2011 at 11:34 AM, elisa carli wrote:
>>
>>> Dear All
>>>
>>> I'd like to perfom a MD simulation on a membrane protein using DLPC or
>>> DPPC system
>>> I've downloaded the API package from this link
>>> http://www.gromacs.org/Downloads/User_contributions/Molecule_topologies
>>>
>>> DPPC.zip and DLPC.zip by schiu
>>>
>>> How can I use them? Where can I get a tutorial or commands illustrating
>>> the use of these packages?
>>>
>>> Thanks in advance
>>>
>>  Here is a rough procedure:
>>
>> http://www.nanoconductor.org/43A1-S3/
>>
>> Took Chiu's  DPPC.zip as an example. We use the speptide.pdb peptide from
>> the gromacs tutorial (it's a bad choice to put it in the dppc, but we just
>> try it).
>>
>> pdb2gmx_g -f speptide.pdb -o speptide.gro
>>
>> choose
>> 9: GROMOS96 43a1 force field
>> 1: SPCsimple point charge, recommended
>>
>> $ tail -1 dppc.gro
>>5.68585   5.60685   6.85739
>>
>> To be as simple as possible here, we use the dimension of the dppc.gro
>>
>> editconf_g -f speptide.gro -o speptide_newbox.gro -center 2.5 2.5 4.2
>> -box  5.68585   5.60685   6.85739
>>
>> now solvate the peptide into the pre-equilibrillium-ed DPPC.gro by
>>
>> genbox_g -cp speptide_newbox.gro -cs dppc.gro -o system.gro -p topol.top
>>
>>
>> Now cp the em.mdp from some_path_to/share/gromacs/tutor/speptide,
>>
>> the purpose of doing a simple energy minimization here just want to "test"
>> the topol.top.
>>
>> it used 43A1-S3 force field (You can download from
>> http://www.nanoconductor.org/43A1-S3/).
>>
>> The head of topol.top:
>> ; Include forcefield parameters
>> #include "ffG43A1-S3.itp"
>> #include "lipids_43A1-S3.itp"
>>
>> The tail of topol.top:
>>
>> [ molecules ]
>> ; Compound#mols
>> Protein 1
>> DPPC 71
>> SOL  3205
>>
>> I manually added DPPC  71.
>>
>> please copy the  lipids_43A1-S3.itpffG43A1-S3.itp
>> ffG43A1-S3par.02.itp from the downloaded 43A1-S3 force field into current
>> directory,
>> extra copy ff_dum.itp from
>> some_path_to/share/gromacs/top/43a1s3.ff/ff_dum.itp into current working
>> directory.
>>
>> I attached all those files in try.tar.gz
>>
>> https://docs.google.com/leaf?id=0B93SVRfpVVg3ZmUxM2ExOTctYTJlNC00MzAxLWI4ZWItNDI2MGM4OThmN2Nj&hl=en_GB
>>
>> mdrun_g -v -deffnm em
>>
>> works well.
>>
>>
>> --
>> Best Regards,
>>
>> lina
>>
>>
>>
>> --
>> gmx-users mailing listgmx-users@gromacs.org
>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>> Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>> Please don't post (un)subscribe requests to the list. Use the
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>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>
>
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-- 
Best Regards,

lina
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Re: [gmx-users] snap shot

2011-10-10 Thread lina

On Sat, Oct 8, 2011 at 2:21 AM, Nilesh Dhumal wrote:

> Hello,
>
> I have a system with 128 emi (cations) and 128 Cl (anions). I run the
> simulation for 20 ns.
>
> I want to save snap-shot at 5ns, 10ns, 15ns and 20ns.
>
trjconv  use -dt 5000

>
> I don't want to save snap shot for 128 ion-pairs. How can I take average
> over 128 ion pairs and save snap shot for a single ion pair.
>
I don't understand the average mean here?
if you wanna get the average.pdb in some time interval try g_rmsf -ox  -b -e

you may wait for some other better answers.


> Basically I want to use classical md geometry for quatum chemical
> calculation.
>
> I am using Gromacs 4.0.7 version.
>
> Thanks
>
> Nilesh
>
>
>
>
>
>
>
>
>
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[gmx-users] A quick Q: How to get the history in make_ndx

2011-10-10 Thread lina

Hi,

How do I use the history input in the make_ndx prompt,

such as before I input

name 32 A2
name 33 A3

up arrow showed me: > ^[[A
Alt+up arrow showed me: > ^[[1;3A

Just curious,

Thanks,
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