[gmx-users] Putting back the images of residues and atoms in the box

[Rohit Farmer]

Hi there,

I am trying to analyze a trajectory and some of the residues and atoms 
are seen as the image across the bound is there anyway to put them back 
in the centre box.


Thanks

Rohit
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Re: [gmx-users] Putting back the images of residues and atoms in the box

[Justin A. Lemkul]

Rohit Farmer wrote:

Hi there,

I am trying to analyze a trajectory and some of the residues and atoms 
are seen as the image across the bound is there anyway to put them back 
in the centre box.




http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions#Suggested_trjconv_workflow

-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] mdrun stuck with PME on BlueGene/P

[Mark Abraham]

On 5/12/2011 9:03 AM, Rongliang Wu wrote:

Dear all,

I have compiled the gromacs 4.5.5 version on BlueGene/P both on the 
front end and bgp using the following script :

with the front end as an example
-- 


version=$1

PREFIX=/home/users/wurl/software/gromacs$version

export ac_cv_sizeof_int=4
export ac_cv_sizeof_long_int=4
export ac_cv_sizeof_long_long_int=8

export CC="xlc_r"
export CFLAGS="-O3 -I/.../fftw3.3/include -qarch=auto -qtune=auto"
export CPPFLAGS="-I/.../fftw3.3/include"
export CXX="xlc_r"
export CXXFLAGS="-O3 -qarch=auto -qtune=auto"

export F77="xlf_r"
export FFLAGS="-O3 -qnoprefetch -qarch=auto -qtune=auto"

export LDFLAGS=" -L/.../fftw3.3/lib"
export LIBS="-lmass"

echo make distclean
make distclean

../configure --prefix=$PREFIX \
 --with-fft=fftw3 \
 --disable-ppc-altivec \
 --without-x \
 --disable-software-sqrt \
 --enable-ppc-sqrt \
 --disable-float \
 --disable-shared

-- 



in both ways, the program gets stuck and doing nothing when using PME:

---
Back Off! I just backed up md.log to ./#md.log.10#
Getting Loaded...
Reading file topol.tpr, VERSION 4.5.5 (double precision)
Loaded with Money
---

I compiled the debug version of mdrun and it told me the problem of fftw

---
Program received signal SIGINT, Interrupt.
[Switching to Thread -134504448 (LWP 31644)]
0x1010dd1c in fftwf_cpy2d ()
--

my compilation of fftw is :
--
version=$1

PREFIX=/home/users/wurl/software/fftw$version

export ac_cv_sizeof_int=4
export ac_cv_sizeof_long_int=4
export ac_cv_sizeof_long_long_int=8

export CC="xlc_r"
export CFLAGS="-O5 -qarch=auto -qtune=auto"
export CXX="xlc_r"
export CXXFLAGS="-O5 -qarch=auto -qtune=auto"

export F77="xlf_r"
export FFLAGS="-O5 -qnoprefetch -qarch=auto -qtune=auto"

export LIBS="-lmass"

echo make distclean
make distclean

../configure --prefix=$PREFIX \
 --disable-fortran \
# --enable-float \

--

When not using PME, the program went well. I also found the same 
problems on the mailing list, but it did not seem to solve the problem 
exactly. Does anyone know how to have this problem solved? I cannot do 
without PME for accurate MD simulations :)


If you want mdrun available on both front and back ends, you will need 
to link each with the corresponding FFTW library. It's not clear to me 
that you are doing that. You will also need to enable MPI to get any 
value out of the back end version.


Mark
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[gmx-users] RMDS calculation

[vferrario]

Dear all,

I need to calculate the RMSD of a protein during time. So that I've  
calculated the trajectory; for the calculation which tool should I  
use? g_rms or g_rmsdist ? Which is the difference between these two  
tools? If I'm right the main difference is that with g_rms the  
structure at the time t is superimposed to the reference structure  
before calculate the RMSD, while with g_rmsdist the RMSD is calculated  
without any superimposition, am I correct?


Valerio


This message was sent using IMP, the Internet Messaging Program.


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Re: [gmx-users] RMDS calculation

[Tsjerk Wassenaar]

Hi Valerio,

Check the help for both tools. That explains it all.
Oh, and you're not correct ;)

Cheers,

Tsjerk

On Mon, Dec 5, 2011 at 4:42 PM,   wrote:
> Dear all,
>
> I need to calculate the RMSD of a protein during time. So that I've
> calculated the trajectory; for the calculation which tool should I use?
> g_rms or g_rmsdist ? Which is the difference between these two tools? If I'm
> right the main difference is that with g_rms the structure at the time t is
> superimposed to the reference structure before calculate the RMSD, while
> with g_rmsdist the RMSD is calculated without any superimposition, am I
> correct?
>
> Valerio
>
> 
> This message was sent using IMP, the Internet Messaging Program.
>
>
> --
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-- 
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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[gmx-users] Re: MSD normalization

[Sławomir Stachura]

Hi,

There is something interesting concerning these MSD calculations. If I treat 
Centre of Mass MSD  if it'd be expressed not in nm^2/ps , but Angstroms^2/ps, I 
get ideally the same results as for mass-weighted ones. And it's true for all 
my three cases, in which I performed simulation of different times. Is that 
possible there is some bug in MSD? Because as for me it looks so
Hope to have someone join the discussion,
   Slawomir





Wiadomość napisana przez Sławomir Stachura w dniu 2011-12-04, o godz. 22:38:

> 
> Hi,
> 
> I was just wondering how MSDs in Gromacs are normalized. I am calculatiing 
> MSDs for my lipid system of different timesteps of simulation and I get much 
> higher results for centre of mass calculations in comparison to mass-weighted 
> one.  And I thought about normalization issue, but I couldn't find any 
> informations concerning that topic in manual.
> I'd be grateful if someone could explain how mean square displacement is 
> normalized.
> 
> Cheers,  
>   Slawomir

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[gmx-users] setenv: Too many arguments

[Mehdi Talebzadeh Farooji]

Dear All,

I have installed gromacs 4.5.5 on ubuntu 11.04, however when I run command 
"source /usr/local/gromacs/bin/GMXRC" it gives the following message without 
doing anything.
"setenv: Too many arguments" The logim shell is tcsh.

Any help or suggestion would be much appreciated.

Mehdi
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[gmx-users] File input/output error pdb2gmx command

[nbhutwal]

Hello.

In GROMACS, within a terminal window on linux ubuntu, I am having trouble
with a pdb2gmx command. The file I am trying to convert to a gmx file is
called 1OTI.pdb. I type in pdb2gmx -f 1OTI.pdb -o 1OTI_processed.gro
-water spce and hit enter. When it prompts me for a forcefield, I enter
the no. corresponding to the forcefield I want, but get a file input
output error: Specifically:

File input/output error:
1OTI.pdb

My initial guess was that it cannot find the file. However, I typed in the
command "pwd" into the terminal and got back /home/nbhutwal. I opened this
directory from my desktop and found that that is where I saved the file
1OTI.pdb, confusing me even more haha. Could someone maybe shed some more
light on this error. Much appreciated!

-Neil

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RE: [gmx-users] File input/output error pdb2gmx command

[Dallas Warren]

Though this looked familiar:

http://lists.gromacs.org/pipermail/gmx-users/2011-November/066557.html

What are the permissions for the file?

Catch ya,

Dr. Dallas Warren
Medicinal Chemistry and Drug Action
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3010
dallas.war...@monash.edu
+61 3 9903 9304
-
When the only tool you own is a hammer, every problem begins to resemble a 
nail. 

> -Original Message-
> From: gmx-users-boun...@gromacs.org [mailto:gmx-users-
> boun...@gromacs.org] On Behalf Of nbhut...@uci.edu
> Sent: Tuesday, 6 December 2011 10:56 AM
> To: gmx-users@gromacs.org
> Subject: [gmx-users] File input/output error pdb2gmx command
> 
> Hello.
> 
> In GROMACS, within a terminal window on linux ubuntu, I am having
> trouble
> with a pdb2gmx command. The file I am trying to convert to a gmx file
> is
> called 1OTI.pdb. I type in pdb2gmx -f 1OTI.pdb -o 1OTI_processed.gro
> -water spce and hit enter. When it prompts me for a forcefield, I enter
> the no. corresponding to the forcefield I want, but get a file input
> output error: Specifically:
> 
> File input/output error:
> 1OTI.pdb
> 
> My initial guess was that it cannot find the file. However, I typed in
> the
> command "pwd" into the terminal and got back /home/nbhutwal. I opened
> this
> directory from my desktop and found that that is where I saved the file
> 1OTI.pdb, confusing me even more haha. Could someone maybe shed some
> more
> light on this error. Much appreciated!
> 
> -Neil
> 
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Re: [gmx-users] File input/output error pdb2gmx command

[Justin A. Lemkul]

nbhut...@uci.edu wrote:

Hello.

In GROMACS, within a terminal window on linux ubuntu, I am having trouble
with a pdb2gmx command. The file I am trying to convert to a gmx file is
called 1OTI.pdb. I type in pdb2gmx -f 1OTI.pdb -o 1OTI_processed.gro
-water spce and hit enter. When it prompts me for a forcefield, I enter
the no. corresponding to the forcefield I want, but get a file input
output error: Specifically:

File input/output error:
1OTI.pdb

My initial guess was that it cannot find the file. However, I typed in the
command "pwd" into the terminal and got back /home/nbhutwal. I opened this
directory from my desktop and found that that is where I saved the file
1OTI.pdb, confusing me even more haha. Could someone maybe shed some more
light on this error. Much appreciated!



Confirm that the file is in the working directory with 'ls' and you'll know for 
sure.  The home directory and desktop are different directories.


-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] Re: MSD normalization

[Mark Abraham]

On 6/12/2011 3:58 AM, Sławomir Stachura wrote:

Hi,

There is something interesting concerning these MSD calculations. If I treat 
Centre of Mass MSD  if it'd be expressed not in nm^2/ps , but Angstroms^2/ps, I 
get ideally the same results as for mass-weighted ones. And it's true for all 
my three cases, in which I performed simulation of different times. Is that 
possible there is some bug in MSD? Because as for me it looks so


I would be amazed if GROMACS did this. Can you copy and paste from your 
terminal to show this?


Mark


Hope to have someone join the discussion,
Slawomir





Wiadomość napisana przez Sławomir Stachura w dniu 2011-12-04, o godz. 22:38:


Hi,

I was just wondering how MSDs in Gromacs are normalized. I am calculatiing MSDs 
for my lipid system of different timesteps of simulation and I get much higher 
results for centre of mass calculations in comparison to mass-weighted one.  
And I thought about normalization issue, but I couldn't find any informations 
concerning that topic in manual.
I'd be grateful if someone could explain how mean square displacement is 
normalized.

Cheers,
   Slawomir


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Re: [gmx-users] setenv: Too many arguments

[Mark Abraham]

On 6/12/2011 8:39 AM, Mehdi Talebzadeh Farooji wrote:

Dear All,

I have installed gromacs 4.5.5 on ubuntu 11.04, however when I run 
command "source /usr/local/gromacs/bin/GMXRC" it gives the following 
message without doing anything.

"setenv: Too many arguments" The logim shell is tcsh.



4.5.5 works for me under tcsh. Perhaps you have a malformed .cshrc? Can 
you source other suitable files?


Mark
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Re: [gmx-users] setenv: Too many arguments

[Mehdi Talebzadeh Farooji]

I installed ARIA and CNS and it works; what do you mean from malformed csh?




 From: Mark Abraham 
To: Discussion list for GROMACS users  
Sent: Monday, December 5, 2011 7:53:17 PM
Subject: Re: [gmx-users] setenv: Too many arguments
 

On 6/12/2011 8:39 AM, Mehdi Talebzadeh Farooji wrote: 
Dear All,
>
>
>I have installed gromacs 4.5.5 on ubuntu 11.04, however when I run command 
>"source /usr/local/gromacs/bin/GMXRC" it gives the following message without 
>doing anything.
>"setenv: Too many arguments" The logim shell is tcsh.
>
4.5.5 works for me under tcsh. Perhaps you have a malformed .cshrc?
Can you source other suitable files?

Mark

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[gmx-users] Simulation in different PH

[Sathish]

Dear all,

How to run simulation in different PH?

Kindly help to fix this problem. Thanks in advance...



-- 

Regards,
N. Sathishkumar,
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Re: [gmx-users] Simulation in different PH

[Justin A. Lemkul]

Sathish wrote:


Dear all,

How to run simulation in different PH?

Kindly help to fix this problem. Thanks in advance...



The concept of "pH" is ill-defined for an MD system, the reasons for which have 
been discussed at length in recent days even (hint: please check the archive 
before posting).  Issues arise with the inability to change protonation, 
inadequate hydronium parameters, inability to model systems of sufficient size 
to even achieve a proper pH, and the list goes on.


The best you might hope for is not a change in "pH" (per strict definition), but 
rather changing the protonation state of titratable groups in your system 
according to pKa.


-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] setenv: Too many arguments

[Mark Abraham]

On 6/12/2011 1:26 PM, Mehdi Talebzadeh Farooji wrote:
I installed ARIA and CNS and it works; what do you mean from malformed 
csh?


I think something is wrong with your environment and in the absence of 
further evidence the problem is likely nothing to do with GROMACS. In 
order to trouble-shoot you need to understand how your shell sets up 
your environment, and this is not the forum for that discussion.


Mark




*From:* Mark Abraham 
*To:* Discussion list for GROMACS users 
*Sent:* Monday, December 5, 2011 7:53:17 PM
*Subject:* Re: [gmx-users] setenv: Too many arguments

On 6/12/2011 8:39 AM, Mehdi Talebzadeh Farooji wrote:

Dear All,

I have installed gromacs 4.5.5 on ubuntu 11.04, however when I run 
command "source /usr/local/gromacs/bin/GMXRC" it gives the following 
message without doing anything.

"setenv: Too many arguments" The logim shell is tcsh.



4.5.5 works for me under tcsh. Perhaps you have a malformed .cshrc? 
Can you source other suitable files?


Mark

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