[gmx-users] distorted structure

[Olga Ivchenko]

Dear gromacs users,

I want to simulate small molecule - choline which is not neutral, it has
uncompensated positive charge. When I transform mol2 file to pdb structure
looks distorted (not correct) in VMD. I added with genion to the system a
negative ions, but the pdb structure is still distorted. Please could you
advice me on this?

best,
Olga
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Re: [gmx-users] distorted structure

[Mark Abraham]

On 30/03/2011 7:50 PM, Olga Ivchenko wrote:

Dear gromacs users,

I want to simulate small molecule - choline which is not neutral, it 
has uncompensated positive charge. When I transform mol2 file to pdb 
structure looks distorted (not correct) in VMD. I added with genion to 
the system a negative ions, but the pdb structure is still distorted. 
Please could you advice me on this?


Either you started with a broken structure, or your conversion broke it. 
Unfortunately there's no way we can tell with this information. Either 
way, the first time you notice a problem, don't plow on regardless - 
it's a great way to waste time and resources.


Mark
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Re: [gmx-users] Strange behavior from g_sas

[Mark Abraham]

On 30/03/2011 5:58 PM, Terry wrote:

Hi, all,

I have four trajectories which I want to analyze Surface on. So I run

for i in 1 2 3 4; do echo -e " non-Water \n Protein " | g_sas -f $i.xtc -s 
$i.tpr -o $i.area.xvg -n index.ndx -q $i.pdb ; done

But the strange thing is, g_sas analyzed the first three trajectories, but gave a 
"segmentation fault for the last one.

The only difference for these trjs is the number of water molecules, hence the 
box size(I used NPT.) . Then I doubt maybe the atom name I used can't be put in 
pdb file (some of them are 5 letters long, and I used gro file since the very 
beginning ). I deleted the -q flag and run g_sas again, seg fault again.

After searching, I did this:
source /usr/local/gromacs/bin/GMXRC
Then g_sas worked fine( without the -q flag).

But I've already sourced GMXRC.bash.


You've either got some other installation of GROMACS that you were 
using, or you changed your input files, or something about the machine 
changed. Unfortunately "segmentation fault" is just a generic error. 
Some idea what the output said before that might clue people in as to 
why that happened.


Mark
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[gmx-users] How to merge 2 top-files

[Ghassen Hassani]

Dear Friends, 
Right now i am working on the docking of a small ligand to a receptor. in order 
to begin md simulations in gromacs, i need to create some files..

I have already docked my ligand to the receptor and i have those files:
   - ligand_receptor.gro
   - posre.itp (for only the receptor !!)
 

I have 2 Questions:

1- How can i expand the posre.itp file to also include the ligand.data ? 
    that means how can i do to create a posre.itp-file for my 
ligand_receptor-komplex ?

2- I have 2 separate top-files: ligand.top (from the prodrg-server) and the 
receptor.top file. How can i "merge" the 2 files and obtain the file 
ligand_receptor.top for the whole ligand-receptor-komplex ?





Many thanx, please email-me on my adress: greendreams1...@yahoo.de

Yours. 




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Re: [gmx-users] How to merge 2 top-files

[Mark Abraham]

On 30/03/2011 8:14 PM, Ghassen Hassani wrote:


Dear Friends,
Right now i am working on the docking of a small ligand to a receptor. 
in order to begin md simulations in gromacs, i need to create some files..


I have already docked my ligand to the receptor and i have those files:
   - ligand_receptor.gro
   - posre.itp (for only the receptor !!)


I have 2 Questions:

1- How can i expand the posre.itp file to also include the ligand.data ?



Don't. The position restraints file is intended to be #included from 
within a [moleculetype]. You have two, so you need two position 
restraint files, each #included from a different, appropriate place. The 
GROMACS tool genrestr can help generate that for the ligand.


that means how can i do to create a posre.itp-file for my 
ligand_receptor-komplex ?




Don't.



2- I have 2 separate top-files: ligand.top (from the prodrg-server) 
and the receptor.top file. How can i "merge" the 2 files and obtain 
the file ligand_receptor.top for the whole ligand-receptor-komplex ?




You need to convert one of your [moleculetype] definitions in one of 
your .top files into an .itp file 
(http://www.gromacs.org/Documentation/File_Formats/.itp_File) and 
#include it suitably from the other. See chapter 5 of the manual for 
details. This is tricky, do your homework first. Note that you should 
take note of the warning here: 
http://www.gromacs.org/Downloads/Related_Software/PRODRG








Many thanx, please email-me on my adress: greendreams1...@yahoo.de

Yours.





No, that is against accepted netiquette. If your question is worth 
answering, then that answer is worth broadcasting and archiving so 
others can learn from it.


Mark
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Re: [gmx-users] Strange behavior from g_sas

[Terry]

Hi Mark,

The output is like this:

WARNING: masses and atomic (Van der Waals) radii will be determined
 based on residue and atom names. These numbers can deviate
 from the correct mass and radius of the atom type.

2565 out of 4931 atoms were classified as hydrophobic

Back Off! I just backed up sas/4.area.xvg to sas/#4.area.xvg.1#

Back Off! I just backed up sas/4.volume.xvg to sas/#4.volume.xvg.1#
There were 372 inconsistent shifts. Check your topology
There were 372 inconsistent shifts. Check your topology
Segmentation fault

I have a periodic molecule, so there are many "inconsistent shifts" lines
which I ignored before.

I still don't understand why g_sas can work with the first three trjs but
the last one in the same for loop.


Terry


On Wed, Mar 30, 2011 at 5:05 PM, Mark Abraham wrote:

> On 30/03/2011 5:58 PM, Terry wrote:
>
>> Hi, all,
>>
>> I have four trajectories which I want to analyze Surface on. So I run
>>
>> for i in 1 2 3 4; do echo -e " non-Water \n Protein " | g_sas -f $i.xtc -s
>> $i.tpr -o $i.area.xvg -n index.ndx -q $i.pdb ; done
>>
>> But the strange thing is, g_sas analyzed the first three trajectories, but
>> gave a "segmentation fault for the last one.
>>
>> The only difference for these trjs is the number of water molecules, hence
>> the box size(I used NPT.) . Then I doubt maybe the atom name I used can't be
>> put in pdb file (some of them are 5 letters long, and I used gro file since
>> the very beginning ). I deleted the -q flag and run g_sas again, seg fault
>> again.
>>
>> After searching, I did this:
>> source /usr/local/gromacs/bin/GMXRC
>> Then g_sas worked fine( without the -q flag).
>>
>> But I've already sourced GMXRC.bash.
>>
>
> You've either got some other installation of GROMACS that you were using,
> or you changed your input files, or something about the machine changed.
> Unfortunately "segmentation fault" is just a generic error. Some idea what
> the output said before that might clue people in as to why that happened.
>
> Mark
> --
> 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 www interface
> or send it to gmx-users-requ...@gromacs.org.
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>
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Re: [gmx-users] Error in GROMACS installation

[Monisha Hajra]

Hi Justin,

I checked carefully. The make command also gave the same error as pasted
below. How should I deal this error?

at' follow
.libs/libxdrf.o:libxdrf.c:(.text+0x31e3): undefined reference to `_xdr_int'
.libs/libxdrf.o:libxdrf.c:(.text+0x340b): undefined reference to `_xdr_int'
.libs/libxdrf.o:libxdrf.c:(.text+0x35a6): undefined reference to `_xdr_int'
.libs/libxdrf.o:libxdrf.c:(.text+0x3785): undefined reference to `_xdr_int'
.libs/libxdrf.o:libxdrf.c:(.text+0x3a01): undefined reference to `_xdr_int'
.libs/gmxfio_xdr.o:gmxfio_xdr.c:(.text+0xeb): undefined reference to
`_xdr_float
'
.libs/gmxfio_xdr.o:gmxfio_xdr.c:(.text+0x126): undefined reference to
`_xdr_doub
le'
.libs/gmxfio_xdr.o:gmxfio_xdr.c:(.text+0x161): undefined reference to
`_xdr_int'

.libs/gmxfio_xdr.o:gmxfio_xdr.c:(.text+0x1ec): undefined reference to
`_xdr_u_ch
ar'
.libs/gmxfio_xdr.o:gmxfio_xdr.c:(.text+0x22f): undefined reference to
`_xdr_u_ch
ar'
.libs/gmxfio_xdr.o:gmxfio_xdr.c:(.text+0x265): undefined reference to
`_xdr_u_ch
ar'
.libs/gmxfio_xdr.o:gmxfio_xdr.c:(.text+0x293): undefined reference to
`_xdr_u_ch
ar'
.libs/gmxfio_xdr.o:gmxfio_xdr.c:(.text+0x2bf): undefined reference to
`_xdr_u_ch
ar'
.libs/gmxfio_xdr.o:gmxfio_xdr.c:(.text+0x309): undefined reference to
`_xdr_u_sh
ort'
.libs/gmxfio_xdr.o:gmxfio_xdr.c:(.text+0x3c4): undefined reference to
`_xdr_doub
le'
.libs/gmxfio_xdr.o:gmxfio_xdr.c:(.text+0x3ed): undefined reference to
`_xdr_vect
or'
.libs/gmxfio_xdr.o:gmxfio_xdr.c:(.text+0x518): undefined reference to
`_xdr_int'

.libs/gmxfio_xdr.o:gmxfio_xdr.c:(.text+0x56c): undefined reference to
`_xdr_int'

.libs/gmxfio_xdr.o:gmxfio_xdr.c:(.text+0x5e1): undefined reference to
`_xdr_int'

.libs/gmxfio_xdr.o:gmxfio_xdr.c:(.text+0x60e): undefined reference to
`_xdr_int'

.libs/gmxfio_xdr.o:gmxfio_xdr.c:(.text+0x63b): undefined reference to
`_xdr_int'

.libs/gmxfio_xdr.o:gmxfio_xdr.c:(.text+0x668): more undefined references to
`_xd
r_int' follow
.libs/gmxfio_xdr.o:gmxfio_xdr.c:(.text+0x764): undefined reference to
`_xdr_doub
le'
.libs/gmxfio_xdr.o:gmxfio_xdr.c:(.text+0x7bd): undefined reference to
`_xdr_floa
t'
.libs/gmxfio_xdr.o:gmxfio_xdr.c:(.text+0x7d4): undefined reference to
`_xdr_vect
or'
.libs/gmxfio_xdr.o:gmxfio_xdr.c:(.text+0x823): undefined reference to
`_xdr_stri
ng'
Creating library file: .libs/libgmx.dll.a
collect2: ld returned 1 exit status
make[4]: *** [libgmx.la] Error 1
make[4]: Leaving directory
`/cygdrive/d/softwares/bioinformatics/gromacs-4.5.4/s
rc/gmxlib'
make[3]: *** [all-recursive] Error 1
make[3]: Leaving directory
`/cygdrive/d/softwares/bioinformatics/gromacs-4.5.4/s
rc/gmxlib'
make[2]: *** [all-recursive] Error 1
make[2]: Leaving directory
`/cygdrive/d/softwares/bioinformatics/gromacs-4.5.4/s
rc'
make[1]: *** [all] Error 2
make[1]: Leaving directory
`/cygdrive/d/softwares/bioinformatics/gromacs-4.5.4/s
rc'
make: *** [all-recursive] Error 1

On Wed, Mar 30, 2011 at 1:54 AM, Justin A. Lemkul  wrote:

>
>
> Monisha Hajra wrote:
>
>> Hi All,
>>
>> I am installing GROMACS using cygwin.
>>
>> I am following the steps as mentioned :
>> http://www.gromacs.org/Downloads/Installation_Instructions/Cygwin_HOWTO
>>
>> *no 5, make install command give the following error in the end :*
>>
>>
> What was your configuration command?  Did "make" work properly?  It's odd
> that "make install" fails if "make" works.  Do you have proper permissions
> to install in this directory?  Configuration and compilation are done
> locally, but installation (if left at default settings) is system-wide.
>
> The actual error message is above what you have posted here.
>
>  ng'
>> Creating library file: .libs/libgmx.dll.a
>> collect2: ld returned 1 exit status
>> make[3]: *** [libgmx.la ] Error 1
>>
>> make[3]: Leaving directory
>> `/cygdrive/d/softwares/bioinformatics/gromacs-4.5.4/s
>> rc/gmxlib'
>> make[2]: *** [install-recursive] Error 1
>> make[2]: Leaving directory
>> `/cygdrive/d/softwares/bioinformatics/gromacs-4.5.4/s
>> rc/gmxlib'
>> make[1]: *** [install-recursive] Error 1
>> make[1]: Leaving directory
>> `/cygdrive/d/softwares/bioinformatics/gromacs-4.5.4/s
>> rc'
>> make: *** [install-recursive] Error 1
>>
>> and* make links command gives the following error:*
>> *
>>
>
> Certainly "make links" will fail if the actual installation failed.
>
> -Justin
>
>  *
>>
>> *
>> $ 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
>> /bin/sh: line 0: cd: /usr/local/gromacs/bin: No such file or directory
>> make: *** [links] Error 1
>>
>> Can anyone de-code thsi error and help me how should I successfully
>> proceed for the same.
>> Thanks in advance.
>>
>> Monisha *
>>
>>
>>
>>
> --
> 
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, V

Re: [gmx-users] Error in GROMACS installation

[Justin A. Lemkul]

Monisha Hajra wrote:

Hi Justin,

I checked carefully. The make command also gave the same error as pasted 
below. How should I deal this error?




For Windows systems, Gromacs needs to use internal XDR definitions (rather than 
those that are available system-wide on most Unix/Linux machines).  It appears 
are not being properly defined.  I have no experience with Windows machines, but 
if you post the following information, perhaps someone can give you some pointers:


1. Your configuration command (and perhaps even the screen output would be 
useful here, too)

2. Your config.h file (in the src subdirectory after configuration finishes)

-Justin


at' follow
.libs/libxdrf.o:libxdrf.c:(.text+0x31e3): undefined reference to `_xdr_int'
.libs/libxdrf.o:libxdrf.c:(.text+0x340b): undefined reference to `_xdr_int'
.libs/libxdrf.o:libxdrf.c:(.text+0x35a6): undefined reference to `_xdr_int'
.libs/libxdrf.o:libxdrf.c:(.text+0x3785): undefined reference to `_xdr_int'
.libs/libxdrf.o:libxdrf.c:(.text+0x3a01): undefined reference to `_xdr_int'
.libs/gmxfio_xdr.o:gmxfio_xdr.c:(.text+0xeb): undefined reference to 
`_xdr_float

'
.libs/gmxfio_xdr.o:gmxfio_xdr.c:(.text+0x126): undefined reference to 
`_xdr_doub

le'
.libs/gmxfio_xdr.o:gmxfio_xdr.c:(.text+0x161): undefined reference to 
`_xdr_int'


.libs/gmxfio_xdr.o:gmxfio_xdr.c:(.text+0x1ec): undefined reference to 
`_xdr_u_ch

ar'
.libs/gmxfio_xdr.o:gmxfio_xdr.c:(.text+0x22f): undefined reference to 
`_xdr_u_ch

ar'
.libs/gmxfio_xdr.o:gmxfio_xdr.c:(.text+0x265): undefined reference to 
`_xdr_u_ch

ar'
.libs/gmxfio_xdr.o:gmxfio_xdr.c:(.text+0x293): undefined reference to 
`_xdr_u_ch

ar'
.libs/gmxfio_xdr.o:gmxfio_xdr.c:(.text+0x2bf): undefined reference to 
`_xdr_u_ch

ar'
.libs/gmxfio_xdr.o:gmxfio_xdr.c:(.text+0x309): undefined reference to 
`_xdr_u_sh

ort'
.libs/gmxfio_xdr.o:gmxfio_xdr.c:(.text+0x3c4): undefined reference to 
`_xdr_doub

le'
.libs/gmxfio_xdr.o:gmxfio_xdr.c:(.text+0x3ed): undefined reference to 
`_xdr_vect

or'
.libs/gmxfio_xdr.o:gmxfio_xdr.c:(.text+0x518): undefined reference to 
`_xdr_int'


.libs/gmxfio_xdr.o:gmxfio_xdr.c:(.text+0x56c): undefined reference to 
`_xdr_int'


.libs/gmxfio_xdr.o:gmxfio_xdr.c:(.text+0x5e1): undefined reference to 
`_xdr_int'


.libs/gmxfio_xdr.o:gmxfio_xdr.c:(.text+0x60e): undefined reference to 
`_xdr_int'


.libs/gmxfio_xdr.o:gmxfio_xdr.c:(.text+0x63b): undefined reference to 
`_xdr_int'


.libs/gmxfio_xdr.o:gmxfio_xdr.c:(.text+0x668): more undefined references 
to `_xd

r_int' follow
.libs/gmxfio_xdr.o:gmxfio_xdr.c:(.text+0x764): undefined reference to 
`_xdr_doub

le'
.libs/gmxfio_xdr.o:gmxfio_xdr.c:(.text+0x7bd): undefined reference to 
`_xdr_floa

t'
.libs/gmxfio_xdr.o:gmxfio_xdr.c:(.text+0x7d4): undefined reference to 
`_xdr_vect

or'
.libs/gmxfio_xdr.o:gmxfio_xdr.c:(.text+0x823): undefined reference to 
`_xdr_stri

ng'
Creating library file: .libs/libgmx.dll.a
collect2: ld returned 1 exit status
make[4]: *** [libgmx.la ] Error 1
make[4]: Leaving directory 
`/cygdrive/d/softwares/bioinformatics/gromacs-4.5.4/s

rc/gmxlib'
make[3]: *** [all-recursive] Error 1
make[3]: Leaving directory 
`/cygdrive/d/softwares/bioinformatics/gromacs-4.5.4/s

rc/gmxlib'
make[2]: *** [all-recursive] Error 1
make[2]: Leaving directory 
`/cygdrive/d/softwares/bioinformatics/gromacs-4.5.4/s

rc'
make[1]: *** [all] Error 2
make[1]: Leaving directory 
`/cygdrive/d/softwares/bioinformatics/gromacs-4.5.4/s

rc'
make: *** [all-recursive] Error 1

On Wed, Mar 30, 2011 at 1:54 AM, Justin A. Lemkul > wrote:




Monisha Hajra wrote:

Hi All,

I am installing GROMACS using cygwin.

I am following the steps as mentioned :
http://www.gromacs.org/Downloads/Installation_Instructions/Cygwin_HOWTO

*no 5, make install command give the following error in the end :*


What was your configuration command?  Did "make" work properly?
 It's odd that "make install" fails if "make" works.  Do you have
proper permissions to install in this directory?  Configuration and
compilation are done locally, but installation (if left at default
settings) is system-wide.

The actual error message is above what you have posted here.

ng'
Creating library file: .libs/libgmx.dll.a
collect2: ld returned 1 exit status
make[3]: *** [libgmx.la  ]
Error 1

make[3]: Leaving directory
`/cygdrive/d/softwares/bioinformatics/gromacs-4.5.4/s
rc/gmxlib'
make[2]: *** [install-recursive] Error 1
make[2]: Leaving directory
`/cygdrive/d/softwares/bioinformatics/gromacs-4.5.4/s
rc/gmxlib'
make[1]: *** [install-recursive] Error 1
make[1]: Leaving directory
`/cygdrive/d/softwares/bioinformatics/gromacs-4.5.4/s
rc'
make: *** [install-recursive] Error 1

and* make links command gives the following error:*

Re: [gmx-users] Strange behavior from g_sas

[Mark Abraham]

On 30/03/2011 9:21 PM, Terry wrote:


Hi Mark,

The output is like this:

WARNING: masses and atomic (Van der Waals) radii will be determined
 based on residue and atom names. These numbers can deviate
 from the correct mass and radius of the atom type.

2565 out of 4931 atoms were classified as hydrophobic

Back Off! I just backed up sas/4.area.xvg to sas/#4.area.xvg.1#

Back Off! I just backed up sas/4.volume.xvg to sas/#4.volume.xvg.1#
There were 372 inconsistent shifts. Check your topology
There were 372 inconsistent shifts. Check your topology
Segmentation fault

I have a periodic molecule, so there are many "inconsistent shifts" 
lines which I ignored before.


I still don't understand why g_sas can work with the first three trjs 
but the last one in the same for loop.


It sounds like g_sas doesn't cope well with periodic molecules. You 
could try the trjconv pbc options, but they need not help you.


Mark


Terry


On Wed, Mar 30, 2011 at 5:05 PM, Mark Abraham > wrote:


On 30/03/2011 5:58 PM, Terry wrote:

Hi, all,

I have four trajectories which I want to analyze Surface on.
So I run

for i in 1 2 3 4; do echo -e " non-Water \n Protein " | g_sas
-f $i.xtc -s $i.tpr -o $i.area.xvg -n index.ndx -q $i.pdb ; done

But the strange thing is, g_sas analyzed the first three
trajectories, but gave a "segmentation fault for the last one.

The only difference for these trjs is the number of water
molecules, hence the box size(I used NPT.) . Then I doubt
maybe the atom name I used can't be put in pdb file (some of
them are 5 letters long, and I used gro file since the very
beginning ). I deleted the -q flag and run g_sas again, seg
fault again.

After searching, I did this:
source /usr/local/gromacs/bin/GMXRC
Then g_sas worked fine( without the -q flag).

But I've already sourced GMXRC.bash.


You've either got some other installation of GROMACS that you were
using, or you changed your input files, or something about the
machine changed. Unfortunately "segmentation fault" is just a
generic error. Some idea what the output said before that might
clue people in as to why that happened.

Mark
-- 
gmx-users mailing list gmx-users@gromacs.org


http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
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[gmx-users] index file

[Elisabeth]

Dear gromacs users,

I am planning to produce C-C rdf for my system and I have difficulty making
the index file with a group of all C in the system, [Carbon] . .If there are
thousands of atoms in the system do I have to go through the top file and
note down C atom numbers and use those numbers to make a group in the index
file? What is the easiest way of doing this using make_ndx features..

Thank you for your hints..
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Re: [gmx-users] index file

[Justin A. Lemkul]

Elisabeth wrote:

Dear gromacs users,

I am planning to produce C-C rdf for my system and I have difficulty 
making the index file with a group of all C in the system, [Carbon] . 
.If there are thousands of atoms in the system do I have to go through 
the top file and note down C atom numbers and use those numbers to make 
a group in the index file? What is the easiest way of doing this using 
make_ndx features..




Using "a C*" at the make_ndx prompt should accomplish what you want.  Type 
"help" at the prompt for more advanced examples.


-Justin


Thank you for your hints..




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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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[gmx-users] Thermal expansion coeff.

[Elisabeth]

Dear all,

I asked this question a few days ago but did not receive a solid answer. Has
anyone tried to produce the properties below? Can you comment on accuracy of
these properties using g_energy?

   Thermal expansion coeff. (NPT): Enthalpy, Vol, Temp
   Isothermal compressibility: Vol, Temp
   Adiabatic bulk modulus: Vol, Temp

Thanks,
Kind regards,
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[gmx-users] gromacs/CPMD. Is LAM mandatory?

[Elena Formoso]

Hi
I am trying to do a QM/MM calculation with gromacs/CPMD. When I try to use a
parallel version of mdrun and CPMD I get a segmentation fault.
I have seen in the examples that LAM is used in runcpmd. It is mandatory for
parallel runs?

Thanks

***
Elena
ETH Zürich and
Università della Svizzera Italiana, USI
Computational Science
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[gmx-users] g_dipole: dipole moment autocorrelation function

[Nilesh Dhumal]

Hello,

I am trying to calculate the dipole moment autocorrelation
function for my system (ionic liquid). I am using gromacs 4.0.7 version.

I run the simulation for 4 ns.  I run the following command to calculate
 the dipole moment autocorrelation function

 g_dipoles -f water.trr -s water.tpr -corr total -c

The function is not geting converge to zero.

I want to use this data for calculation of power spectra by fourier
transfom of dipole moment autocorrelation function.

Can you tell why its not geting converge to zero?


Thanks

Nilesh



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[gmx-users] g_energy -ravg option

[simon sham]

Hi,
I need to calculate a running average on pressure, and have problem in using 
the -ravg option in g_energy command:
I have tried the followings:

1. g_energy -f file.edr -ravg ravg.xvg -o pressure.xvg
2. g_energy -f file.edr -ravg -o pressure.xvg

I could get the fluctuations in pressure.xvg, but not the running averages.

Any help is appreciated in advance.

Simon Sham

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Re: [gmx-users] g_dipole: dipole moment autocorrelation function

[David van der Spoel]

On 2011-03-30 18.54, Nilesh Dhumal wrote:

Hello,

I am trying to calculate the dipole moment autocorrelation
function for my system (ionic liquid). I am using gromacs 4.0.7 version.

I run the simulation for 4 ns.  I run the following command to calculate
  the dipole moment autocorrelation function

  g_dipoles -f water.trr -s water.tpr -corr total -c

The function is not geting converge to zero.

I want to use this data for calculation of power spectra by fourier
transfom of dipole moment autocorrelation function.

Can you tell why its not geting converge to zero?

You have to simulate at least a few 10s of ns for such slow liquids to 
converge. Alternatively you can average over many independent 
simulations (10s).


Thanks

Nilesh






--
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205.
sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se
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Re: [gmx-users] g_energy -ravg option

[Justin A. Lemkul]

simon sham wrote:

Hi,
I need to calculate a running average on pressure, and have problem in 
using the -ravg option in g_energy command:

I have tried the followings:

1. g_energy -f file.edr -ravg ravg.xvg -o pressure.xvg
2. g_energy -f file.edr -ravg -o pressure.xvg

I could get the fluctuations in pressure.xvg, but not the running averages.



The -ravg option is to produce running averages of free energy differences 
between states provided in two .edr files (-f and -f2).


Xmgrace can produce running averages for the data in the .xvg file.

-Justin


Any help is appreciated in advance.

Simon Sham



--


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] g_dipole: dipole moment autocorrelation function

[Nilesh Dhumal]

Thanks.
How can I take average.

How much long I should run the simulation.

Nilesh

On Wed, March 30, 2011 12:59 pm, David van der Spoel wrote:
> On 2011-03-30 18.54, Nilesh Dhumal wrote:
>
>> Hello,
>>
>>
>> I am trying to calculate the dipole moment autocorrelation
>> function for my system (ionic liquid). I am using gromacs 4.0.7 version.
>>
>>
>> I run the simulation for 4 ns.  I run the following command to
>> calculate the dipole moment autocorrelation function
>>
>> g_dipoles -f water.trr -s water.tpr -corr total -c
>>
>> The function is not geting converge to zero.
>>
>>
>> I want to use this data for calculation of power spectra by fourier
>> transfom of dipole moment autocorrelation function.
>>
>> Can you tell why its not geting converge to zero?
>>
>>
> You have to simulate at least a few 10s of ns for such slow liquids to
> converge. Alternatively you can average over many independent simulations
> (10s).
>
>>
>> Thanks
>>
>>
>> Nilesh
>>
>>
>>
>>
>
>
> --
> David van der Spoel, Ph.D., Professor of Biology
> Dept. of Cell & Molec. Biol., Uppsala University.
> Box 596, 75124 Uppsala, Sweden. Phone:+46184714205.
> sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
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> http://www.gromacs.org/Support/Mailing_Lists
>
>
>


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[gmx-users] Splitted DMPC bilayer

[Dr. Ramón Garduño-Juárez]

Dear all,
Dear Justin,

This time I want to ask the gurus about this problem I encountered in 
the Equilibration step of my system made of 3 individual (small) protein 
chains in a solvated DMPC bilayer, no ions present since the protein 
system is neutral...


Following the tutorial I started with

 make_ndx_d -f em_after_solv.gro -o index_after_solv.ndx

for which I got the following list:
-
Reading structure file
Going to read 0 old index file(s)
Analysing residue names:
There are:   129Protein residues
There are:   123  Other residues
There are:  3215  Water residues
Analysing Protein...
Analysing residues not classified as Protein/DNA/RNA/Water and splitting 
into groups...


  0 System  : 16649 atoms
  1 Protein :  1346 atoms
  2 Protein-H   :  1025 atoms
  3 C-alpha :   129 atoms
  4 Backbone:   387 atoms
  5 MainChain   :   519 atoms
  6 MainChain+Cb:   636 atoms
  7 MainChain+H :   649 atoms
  8 SideChain   :   697 atoms
  9 SideChain-H :   506 atoms
 10 Prot-Masses :  1346 atoms
 11 non-Protein : 15303 atoms
 12 Other   :  5658 atoms
 13 DMPC:  5658 atoms
 14 Water   :  9645 atoms
 15 SOL :  9645 atoms
 16 non-Water   :  7004 atoms
-

Since I did not add ions I have formed a (merged) group named SOL_SOL 
after chosing  15 | 15 , and another merged group named Protein_DMPC by 
choosing  1 | 13...


Next, I started the NVT equilibration with:

grompp_d  -f nvt.mdp  -c em_after_solv.gro  -p topol_mod_lip_solv.top  
-n index_after_solv.ndx  -o nvt.tpr


The nvt.mpd file is the same as the one given in the tutorial, the only 
changes I made were:


tc-grps= Protein DMPC SOL_SOL
and
comm-grps= Protein_DMPC SOL_SOL

After this I ran

mdrun_mpi_d  -v  -deffnm nvt

When this process is finished I looked at the resulting nvt.gro file and 
found the following:


1) The 3 protein chains complex is fine, at the center of the box as it 
should be, but
2) The 2 DMPC layer are separated (splitted) leaving a large gap between 
them forming a )( shape where the top and bottom of this figure contain 
one layer of DMPC plus water molecules, while in the narrow section the 
protein complex is found... In the void between the two DMPC layers no 
water molecules are present...  Very odd!...


Please advice...

Cheers,
Ramon Garduno
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Re: [gmx-users] g_dipole: dipole moment autocorrelation function

[David van der Spoel]

On 2011-03-30 20.16, Nilesh Dhumal wrote:

Thanks.
How can I take average.

summing up and dividing by the number of sims.


How much long I should run the simulation.

until the average converges.


Nilesh

On Wed, March 30, 2011 12:59 pm, David van der Spoel wrote:

On 2011-03-30 18.54, Nilesh Dhumal wrote:


Hello,


I am trying to calculate the dipole moment autocorrelation
function for my system (ionic liquid). I am using gromacs 4.0.7 version.


I run the simulation for 4 ns.  I run the following command to
calculate the dipole moment autocorrelation function

g_dipoles -f water.trr -s water.tpr -corr total -c

The function is not geting converge to zero.


I want to use this data for calculation of power spectra by fourier
transfom of dipole moment autocorrelation function.

Can you tell why its not geting converge to zero?



You have to simulate at least a few 10s of ns for such slow liquids to
converge. Alternatively you can average over many independent simulations
(10s).



Thanks


Nilesh







--
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell&  Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205.
sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se --
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--
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205.
sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se
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Re: [gmx-users] Splitted DMPC bilayer

[Justin A. Lemkul]

Dr. Ramón Garduño-Juárez wrote:

Dear all,
Dear Justin,

This time I want to ask the gurus about this problem I encountered in 
the Equilibration step of my system made of 3 individual (small) protein 
chains in a solvated DMPC bilayer, no ions present since the protein 
system is neutral...


Following the tutorial I started with

 make_ndx_d -f em_after_solv.gro -o index_after_solv.ndx

for which I got the following list:
-
Reading structure file
Going to read 0 old index file(s)
Analysing residue names:
There are:   129Protein residues
There are:   123  Other residues
There are:  3215  Water residues
Analysing Protein...
Analysing residues not classified as Protein/DNA/RNA/Water and splitting 
into groups...


  0 System  : 16649 atoms
  1 Protein :  1346 atoms
  2 Protein-H   :  1025 atoms
  3 C-alpha :   129 atoms
  4 Backbone:   387 atoms
  5 MainChain   :   519 atoms
  6 MainChain+Cb:   636 atoms
  7 MainChain+H :   649 atoms
  8 SideChain   :   697 atoms
  9 SideChain-H :   506 atoms
 10 Prot-Masses :  1346 atoms
 11 non-Protein : 15303 atoms
 12 Other   :  5658 atoms
 13 DMPC:  5658 atoms
 14 Water   :  9645 atoms
 15 SOL :  9645 atoms
 16 non-Water   :  7004 atoms
-

Since I did not add ions I have formed a (merged) group named SOL_SOL 


Why would you merge solvent with itself?

after chosing  15 | 15 , and another merged group named Protein_DMPC by 
choosing  1 | 13...


Next, I started the NVT equilibration with:

grompp_d  -f nvt.mdp  -c em_after_solv.gro  -p topol_mod_lip_solv.top  
-n index_after_solv.ndx  -o nvt.tpr


The nvt.mpd file is the same as the one given in the tutorial, the only 
changes I made were:


tc-grps= Protein DMPC SOL_SOL
and
comm-grps= Protein_DMPC SOL_SOL



I would think that using this weird SOL_SOL group would create problems related 
to degrees of freedom, etc.  If you have no ions, there is no need to merge any 
sort of solvent-related groups.



After this I ran

mdrun_mpi_d  -v  -deffnm nvt

When this process is finished I looked at the resulting nvt.gro file and 
found the following:


1) The 3 protein chains complex is fine, at the center of the box as it 
should be, but
2) The 2 DMPC layer are separated (splitted) leaving a large gap between 
them forming a )( shape where the top and bottom of this figure contain 
one layer of DMPC plus water molecules, while in the narrow section the 
protein complex is found... In the void between the two DMPC layers no 
water molecules are present...  Very odd!...


Please advice...



This is covered in the "Advanced Troubleshooting" section of my tutorial:

http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/advanced_troubleshooting.html

-Justin


Cheers,
Ramon Garduno



--


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] Heat of vap

[Elisabeth]

Dear all,

I intend to obtain vaporization heat per volume for a *pure alkane system*.
Here is the steps I am taking. Please correct me.

1- Obtain total energy of system (kinetic+potential) and divide by number of
molecules to obtain energy per mol of molecules. g_energy -f *.edr -nmol XXX
2- Obtain total energy of a single molecule (use pbc).
3- Subtract step 2 from step 1.
4- Divide by simulation box volume.

My questions is:

in step 2 : what should be the box size? The same size as in 1 or it does
not matter? (step 1 is done for the actual denstiy)

Thanking you all,
Regards,
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Re: [gmx-users] Heat of vap

[David van der Spoel]

On 2011-03-30 21.22, Elisabeth wrote:

Dear all,

I intend to obtain vaporization heat per volume for a /pure alkane
system/.  Here is the steps I am taking. Please correct me.

1- Obtain total energy of system (kinetic+potential) and divide by
number of molecules to obtain energy per mol of molecules. g_energy -f
*.edr -nmol XXX
2- Obtain total energy of a single molecule (use pbc).
3- Subtract step 2 from step 1.
4- Divide by simulation box volume.

My questions is:

in step 2 : what should be the box size? The same size as in 1 or it
does not matter? (step 1 is done for the actual denstiy)

do turn off all pbc and cutoff for that one.


Thanking you all,
Regards,




--
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205.
sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se
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Re: [gmx-users] Heat of vap

[Justin A. Lemkul]

Elisabeth wrote:

Dear all,

I intend to obtain vaporization heat per volume for a /pure alkane 
system/.  Here is the steps I am taking. Please correct me.


1- Obtain total energy of system (kinetic+potential) and divide by 
number of molecules to obtain energy per mol of molecules. g_energy -f 
*.edr -nmol XXX

2- Obtain total energy of a single molecule (use pbc).
3- Subtract step 2 from step 1.
4- Divide by simulation box volume.

My questions is:

in step 2 : what should be the box size? The same size as in 1 or it 
does not matter? (step 1 is done for the actual denstiy)




More troubling, how does one define the energy of a molecule?  If you use any 
sort of long-range algorithms (especially PME, but also dispersion correction), 
you can't simply decompose the system like this.


In the derivation of recent Gromos96 parameter sets, the heat of vaporization is 
quite simple:


DHvap =  -  + RT

I have seen this equation used in a number of other studies, as well.

-Justin


Thanking you all,
Regards,



--


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] Help on umbrella sampling

[raghuvir]

Dear Users and Developers

I am trying to execute md_pull.mdp {given below} on a small molecule  
embedded at the core of lipid bilayer.  I have tried to modify the  
md_pull.mdp from the Tutorial by Justin Lemkul on Umbrella sampling.   
I encounter LINCS warning  (1000) after about 100-110 ps of the  
simulation resulting in termination of mdrun. This occurs when the  
small molecule is near the polar heads.  I understand the system is  
exploding.


I have minimized the system, followed by anneal to 323K then nvt and  
npt after which I perform the md_pull.  How can I soften the core {as  
mentioned in the errors on www.gromacs.org} or any other alternative  
is there adding lincs warning to mdp file {I am not aware}


Following is the md_pull.mdp file as modified;
X
title   = Umbrella pulling simulation
define  = -DPOSRES_DPPC
; Run parameters
integrator  = md
dt  = 0.002
tinit   = 0
nsteps  = 10; 200 ps
nstcomm = 1
; Output parameters
nstxout = 5000  ; every 10 ps
nstvout = 5000
nstfout = 500
nstxtcout   = 500   ; every 1 ps
nstenergy   = 500
; Bond parameters
constraint_algorithm= lincs
constraints = all-bonds
continuation= yes   ; continuing from NPT
; Single-range cutoff scheme
nstlist = 5
ns_type = grid
rlist   = 1.4
rcoulomb= 1.4
rvdw= 1.4
; PME electrostatics parameters
coulombtype = PME
fourierspacing  = 0.12
fourier_nx  = 0
fourier_ny  = 0
fourier_nz  = 0
pme_order   = 4
ewald_rtol  = 1e-5
optimize_fft= yes
; Berendsen temperature coupling is on in two groups
Tcoupl  =   Nose-Hoover
tc_grps =   TPF DPPCSOL
tau_t   =   0.1 0.1 0.1
ref_t   =   323 323 323
; Pressure coupling is on
pcoupl  = Parrinello-Rahman ; Pressure coupling on in NPT
pcoupltype	= semiisotropic		; uniform scaling of x-y box vectors,  
independent z

tau_p   = 2.0   ; time constant, in ps
ref_p   = 1.0   1.0 ; reference pressure, x-y, z 
(in bar)
compressibility = 4.5e-54.5e-5  ; isothermal compressibility, bar^-1
; Generate velocities is off
gen_vel = no
; Periodic boundary conditions are on in all directions
pbc = xyz
; Long-range dispersion correction
DispCorr= EnerPres
; Pull code
pull= umbrella
pull_geometry   = distance
pull_dim= N N Y
pull_start  = yes   ; define initial COM distance > 0
pull_ngroups= 1
pull_group0 = DPPC
pull_group1 = TPF
pull_rate1  = 0.01  ; 0.01 nm per ps = 10 nm per ns
pull_k1 = 1000  ; kJ mol^-1 nm^-2
XX
Please help me

Thanks N Regards

Raghuvir

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Re: [gmx-users] Help on umbrella sampling

[Justin A. Lemkul]

raghu...@bcpindia.org wrote:

Dear Users and Developers

I am trying to execute md_pull.mdp {given below} on a small molecule 
embedded at the core of lipid bilayer.  I have tried to modify the 
md_pull.mdp from the Tutorial by Justin Lemkul on Umbrella sampling.  I 
encounter LINCS warning  (1000) after about 100-110 ps of the simulation 
resulting in termination of mdrun. This occurs when the small molecule 
is near the polar heads.  I understand the system is exploding.


I have minimized the system, followed by anneal to 323K then nvt and npt 
after which I perform the md_pull.  How can I soften the core {as 
mentioned in the errors on www.gromacs.org} or any other alternative is 
there adding lincs warning to mdp file {I am not aware}




"Soft core" is a mechanism by which Lennard-Jones interactions are modified 
while doing decoupling/annihilation calculations.  This point is not relevant here.


I see that you're restraining the lipids in some way.  Which atoms are 
restrained?  In which directions?  Why are you restraining them?  I would assume 
that as a molecule is pulled through your membrane, any artificial forces that 
work against one another would cause instability.


-Justin


Following is the md_pull.mdp file as modified;
X
title= Umbrella pulling simulation
define= -DPOSRES_DPPC
; Run parameters
integrator= md
dt= 0.002
tinit= 0
nsteps= 10; 200 ps
nstcomm= 1
; Output parameters
nstxout= 5000; every 10 ps
nstvout= 5000
nstfout= 500
nstxtcout= 500; every 1 ps
nstenergy= 500
; Bond parameters
constraint_algorithm = lincs
constraints= all-bonds
continuation = yes; continuing from NPT
; Single-range cutoff scheme
nstlist= 5
ns_type= grid
rlist= 1.4
rcoulomb= 1.4
rvdw= 1.4
; PME electrostatics parameters
coulombtype= PME
fourierspacing  = 0.12
fourier_nx= 0
fourier_ny = 0
fourier_nz= 0
pme_order= 4
ewald_rtol= 1e-5
optimize_fft= yes
; Berendsen temperature coupling is on in two groups
Tcoupl =Nose-Hoover
tc_grps=TPFDPPCSOL
tau_t=0.10.10.1
ref_t=323323323
; Pressure coupling is on
pcoupl= Parrinello-Rahman; Pressure coupling on in NPT
pcoupltype= semiisotropic; uniform scaling of x-y box 
vectors, independent z

tau_p= 2.0; time constant, in ps
ref_p= 1.01.0; reference pressure, x-y, z 
(in bar)

compressibility = 4.5e-54.5e-5; isothermal compressibility, bar^-1
; Generate velocities is off
gen_vel= no
; Periodic boundary conditions are on in all directions
pbc= xyz
; Long-range dispersion correction
DispCorr= EnerPres
; Pull code
pull= umbrella
pull_geometry= distance
pull_dim= N N Y
pull_start= yes; define initial COM distance > 0
pull_ngroups= 1
pull_group0= DPPC
pull_group1= TPF
pull_rate1= 0.01; 0.01 nm per ps = 10 nm per ns
pull_k1= 1000; kJ mol^-1 nm^-2
XX
Please help me

Thanks N Regards

Raghuvir



--


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] the total charge of system is not an integer

[ahmet yıldırım]

Dear users,

Before energy minimization step , I performed the preprosessing step using
grompp .
However, there are two note that :

*NOTE 1 [file topol.top, line 52]:*
  System has non-zero total charge: -1.50e+01

*NOTE 2 [file topol.top]:*
  The largest charge group contains 11 atoms.
  Since atoms only see each other when the centers of geometry of the charge
  groups they belong to are within the cut-off distance, too large charge
  groups can lead to serious cut-off artifacts.
  For efficiency and accuracy, charge group should consist of a few atoms.
  For all-atom force fields use: CH3, CH2, CH, NH2, NH, OH, CO2, CO, etc.
*
PS: *TRS and EDO are not aminoacid*

TRS.itp:*
..
[ moleculetype ]
; Name nrexcl
TRS  3

[ atoms ]
;   nr  type  resnr resid  atom  cgnr   charge mass
 1OA 1  TRS  O1 1   -0.119  15.9994
 2 H 1  TRS H13 10.032   1.0080
 3   CH2 1  TRS  C1 10.087  14.0270
 4  CCl4 1  TRS   C 20.055  12.0110
 5   CH2 1  TRS  C3 20.049  14.0270
 6OA 1  TRS  O3 2   -0.205  15.9994
 7 H 1  TRS H33 20.019   1.0080
 8NL 1  TRS   N 20.206  14.0067
 9 H 1  TRS  H2 20.004   1.0080
10 H 1  TRS  H3 20.004   1.0080
11 H 1  TRS  H1 20.004   1.0080
12   CH2 1  TRS  C2 20.050  14.0270
13OA 1  TRS  O2 2   -0.205  15.9994
14 H 1  TRS H23 20.019   1.0080
...

*EDO.itp*
...
[ moleculetype ]
; Name nrexcl
EDO  3

[ atoms ]
;   nr  type  resnr resid  atom  cgnr   charge mass
 1OA 1  EDO OAB 1   -0.111  15.9994
 2 H 1  EDO HAE 10.031   1.0080
 3   CH2 1  EDO CAA 10.080  14.0270
 4   CH2 1  EDO CAC 10.080  14.0270
 5OA 1  EDO OAD 1   -0.111  15.9994
 6 H 1  EDO HAF 10.031   1.0080
...
*
topol.top:*
..
; Include water topology
#include "gromos43a1.ff/spc.itp"
#include "TRS.itp"
#include "EDO.itp"
..
[ molecules ]
; Compound#mols
Protein_chain_A 1
Protein_chain_B 1
SOL   185
SOL   143
TRS1
EDO1
SOL 44125
*
Conf.gro:*
MTA/SAH NUCLEOSIDASE; 5 NUCLEOSIDASE
 5354
2GLN  N1   1.458  -1.158   0.739
2GLN H12   1.520  -1.083   0.763
...
  485HOHHW1 5333   0.221  -3.864  -2.291
  485HOHHW2 5334   0.303  -3.946  -2.407
1TRS  O1   1  -3.812  -0.471  -2.002
1TRS  H13  2  -3.865  -0.443  -1.922
1TRS  C1   3  -3.672  -0.469  -1.971
1TRS  C4  -3.635  -0.571  -1.863
1TRS  C3   5  -3.711  -0.547  -1.731
1TRS  O3   6  -3.694  -0.414  -1.679
1TRS  H33  7  -3.746  -0.404  -1.594
1TRS  N8  -3.673  -0.705  -1.911
1TRS  H2   9  -3.625  -0.725  -1.996
1TRS  H3  10  -3.771  -0.707  -1.927
1TRS  H1  11  -3.649  -0.774  -1.842
1TRS  C2  12  -3.483  -0.573  -1.840
1TRS  O2  13  -3.428  -0.445  -1.806
1TRS  H23 14  -3.470  -0.412  -1.722
1EDO  OAB  1   0.307  -2.792   0.149
1EDO  HAE  2   0.390  -2.826   0.104
1EDO  CAA  3   0.239  -2.901   0.212
1EDO  CAC  4   0.111  -2.851   0.281
1EDO  OAD  5   0.144  -2.763   0.388
1EDO  HAF  6   0.060  -2.731   0.432
   8.13100   7.04165  13.54850   0.0   0.0  -4.06550   0.0
0.0   0.0

How can I fixed these notes(note 1 and note 2)?

Thanks in advance
-- 
Ahmet YILDIRIM
-- 
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Re: [gmx-users] the total charge of system is not an integer

[Tsjerk Wassenaar]

Hi Ahmet,

As suggested, it's better to break up your molecule into smaller
charge groups. Note that charge groups don't need to have zero charge,
nor integer charge. In your case, I'd suggest two COH groups for EDO,
which will have zero net charge each, and for TRS I'd take the COH
groups as separate charge groups. I also note that the COH groups,
although chemically identical - H3NC(COH)3, right?-, have different
charges. That doesn't seem proper.

Hope it helps,

Tsjerk

2011/3/31 ahmet yıldırım :
> Dear users,
>
> Before energy minimization step , I performed the preprosessing step using
> grompp .
> However, there are two note that :
>
> NOTE 1 [file topol.top, line 52]:
>   System has non-zero total charge: -1.50e+01
>
> NOTE 2 [file topol.top]:
>   The largest charge group contains 11 atoms.
>   Since atoms only see each other when the centers of geometry of the charge
>   groups they belong to are within the cut-off distance, too large charge
>   groups can lead to serious cut-off artifacts.
>   For efficiency and accuracy, charge group should consist of a few atoms.
>   For all-atom force fields use: CH3, CH2, CH, NH2, NH, OH, CO2, CO, etc.
>
> PS: TRS and EDO are not aminoacid
>
> TRS.itp:
> ..
> [ moleculetype ]
> ; Name nrexcl
> TRS  3
>
> [ atoms ]
> ;   nr  type  resnr resid  atom  cgnr   charge mass
>  1    OA 1  TRS  O1 1   -0.119  15.9994
>  2 H 1  TRS H13 1    0.032   1.0080
>  3   CH2 1  TRS  C1 1    0.087  14.0270
>  4  CCl4 1  TRS   C 2    0.055  12.0110
>  5   CH2 1  TRS  C3 2    0.049  14.0270
>  6    OA 1  TRS  O3 2   -0.205  15.9994
>  7 H 1  TRS H33 2    0.019   1.0080
>  8    NL 1  TRS   N 2    0.206  14.0067
>  9 H 1  TRS  H2 2    0.004   1.0080
>     10 H 1  TRS  H3 2    0.004   1.0080
>     11 H 1  TRS  H1 2    0.004   1.0080
>     12   CH2 1  TRS  C2 2    0.050  14.0270
>     13    OA 1  TRS  O2 2   -0.205  15.9994
>     14 H 1  TRS H23 2    0.019   1.0080
> ...
>
> EDO.itp
> ...
> [ moleculetype ]
> ; Name nrexcl
> EDO  3
>
> [ atoms ]
> ;   nr  type  resnr resid  atom  cgnr   charge mass
>  1    OA 1  EDO OAB 1   -0.111  15.9994
>  2 H 1  EDO HAE 1    0.031   1.0080
>  3   CH2 1  EDO CAA 1    0.080  14.0270
>  4   CH2 1  EDO CAC 1    0.080  14.0270
>  5    OA 1  EDO OAD 1   -0.111  15.9994
>  6 H 1  EDO HAF 1    0.031   1.0080
> ...
>
> topol.top:
> ..
> ; Include water topology
> #include "gromos43a1.ff/spc.itp"
> #include "TRS.itp"
> #include "EDO.itp"
> ..
> [ molecules ]
> ; Compound    #mols
> Protein_chain_A 1
> Protein_chain_B 1
> SOL   185
> SOL   143
> TRS    1
> EDO    1
> SOL 44125
>
> Conf.gro:
> MTA/SAH NUCLEOSIDASE; 5 NUCLEOSIDASE
>  5354
>     2GLN  N    1   1.458  -1.158   0.739
>     2GLN H1    2   1.520  -1.083   0.763
> ...
>   485HOH    HW1 5333   0.221  -3.864  -2.291
>   485HOH    HW2 5334   0.303  -3.946  -2.407
>     1TRS  O1   1  -3.812  -0.471  -2.002
>     1TRS  H13  2  -3.865  -0.443  -1.922
>     1TRS  C1   3  -3.672  -0.469  -1.971
>     1TRS  C    4  -3.635  -0.571  -1.863
>     1TRS  C3   5  -3.711  -0.547  -1.731
>     1TRS  O3   6  -3.694  -0.414  -1.679
>     1TRS  H33  7  -3.746  -0.404  -1.594
>     1TRS  N    8  -3.673  -0.705  -1.911
>     1TRS  H2   9  -3.625  -0.725  -1.996
>     1TRS  H3  10  -3.771  -0.707  -1.927
>     1TRS  H1  11  -3.649  -0.774  -1.842
>     1TRS  C2  12  -3.483  -0.573  -1.840
>     1TRS  O2  13  -3.428  -0.445  -1.806
>     1TRS  H23 14  -3.470  -0.412  -1.722
>     1EDO  OAB  1   0.307  -2.792   0.149
>     1EDO  HAE  2   0.390  -2.826   0.104
>     1EDO  CAA  3   0.239  -2.901   0.212
>     1EDO  CAC  4   0.111  -2.851   0.281
>     1EDO  OAD  5   0.144  -2.763   0.388
>     1EDO  HAF  6   0.060  -2.731   0.432
>    8.13100   7.04165  13.54850   0.0   0.0  -4.06550   0.0
> 0.0   0.0
>
> How can I fixed these notes(note 1 and note 2)?
>
> Thanks in advance
> --
> Ahmet YILDIRIM
>
> --
> 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
>



-- 
Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular R

Re: [gmx-users] the total charge of system is not an integer

[Mark Abraham]

On 31/03/2011 5:18 PM, ahmet y?ld?r?m wrote:

Dear users,

Before energy minimization step , I performed the preprosessing step 
using grompp .

However, there are two note that :

*_NOTE 1 [file topol.top, line 52]:_*
  System has non-zero total charge: -1.50e+01


This is an integer. See 
http://en.wikipedia.org/wiki/Scientific_notation#E_notation and 
http://www.gromacs.org/Documentation/Floating_Point_Arithmetic



_*NOTE 2 [file topol.top]:*_
  The largest charge group contains 11 atoms.
  Since atoms only see each other when the centers of geometry of the 
charge

  groups they belong to are within the cut-off distance, too large charge
  groups can lead to serious cut-off artifacts.
  For efficiency and accuracy, charge group should consist of a few atoms.
  For all-atom force fields use: CH3, CH2, CH, NH2, NH, OH, CO2, CO, etc.


See Tsjerk's email.

Mark


*
PS: *TRS and EDO are not aminoacid*

_TRS.itp:_*
..
[ moleculetype ]
; Name nrexcl
TRS  3

[ atoms ]
;   nr  type  resnr resid  atom  cgnr   charge mass
 1OA 1  TRS  O1 1   -0.119  15.9994
 2 H 1  TRS H13 10.032   1.0080
 3   CH2 1  TRS  C1 10.087  14.0270
 4  CCl4 1  TRS   C 20.055  12.0110
 5   CH2 1  TRS  C3 20.049  14.0270
 6OA 1  TRS  O3 2   -0.205  15.9994
 7 H 1  TRS H33 20.019   1.0080
 8NL 1  TRS   N 20.206  14.0067
 9 H 1  TRS  H2 20.004   1.0080
10 H 1  TRS  H3 20.004   1.0080
11 H 1  TRS  H1 20.004   1.0080
12   CH2 1  TRS  C2 20.050  14.0270
13OA 1  TRS  O2 2   -0.205  15.9994
14 H 1  TRS H23 20.019   1.0080
...

_*EDO.itp*_
...
[ moleculetype ]
; Name nrexcl
EDO  3

[ atoms ]
;   nr  type  resnr resid  atom  cgnr   charge mass
 1OA 1  EDO OAB 1   -0.111  15.9994
 2 H 1  EDO HAE 10.031   1.0080
 3   CH2 1  EDO CAA 10.080  14.0270
 4   CH2 1  EDO CAC 10.080  14.0270
 5OA 1  EDO OAD 1   -0.111  15.9994
 6 H 1  EDO HAF 10.031   1.0080
...
_*
topol.top:*_
..
; Include water topology
#include "gromos43a1.ff/spc.itp"
#include "TRS.itp"
#include "EDO.itp"
..
[ molecules ]
; Compound#mols
Protein_chain_A 1
Protein_chain_B 1
SOL   185
SOL   143
TRS1
EDO1
SOL 44125
*_
Conf.gro:_*
MTA/SAH NUCLEOSIDASE; 5 NUCLEOSIDASE
 5354
2GLN  N1   1.458  -1.158   0.739
2GLN H12   1.520  -1.083   0.763
...
  485HOHHW1 5333   0.221  -3.864  -2.291
  485HOHHW2 5334   0.303  -3.946  -2.407
1TRS  O1   1  -3.812  -0.471  -2.002
1TRS  H13  2  -3.865  -0.443  -1.922
1TRS  C1   3  -3.672  -0.469  -1.971
1TRS  C4  -3.635  -0.571  -1.863
1TRS  C3   5  -3.711  -0.547  -1.731
1TRS  O3   6  -3.694  -0.414  -1.679
1TRS  H33  7  -3.746  -0.404  -1.594
1TRS  N8  -3.673  -0.705  -1.911
1TRS  H2   9  -3.625  -0.725  -1.996
1TRS  H3  10  -3.771  -0.707  -1.927
1TRS  H1  11  -3.649  -0.774  -1.842
1TRS  C2  12  -3.483  -0.573  -1.840
1TRS  O2  13  -3.428  -0.445  -1.806
1TRS  H23 14  -3.470  -0.412  -1.722
1EDO  OAB  1   0.307  -2.792   0.149
1EDO  HAE  2   0.390  -2.826   0.104
1EDO  CAA  3   0.239  -2.901   0.212
1EDO  CAC  4   0.111  -2.851   0.281
1EDO  OAD  5   0.144  -2.763   0.388
1EDO  HAF  6   0.060  -2.731   0.432
   8.13100   7.04165  13.54850   0.0   0.0  -4.06550   
0.0   0.0   0.0


How can I fixed these notes(note 1 and note 2)?

Thanks in advance
--
Ahmet YILDIRIM


-- 
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[gmx-users] Re: gmx-users Digest, Vol 83, Issue 217

[Raghuvir R S Pissurlenkar]

Thanks Justin

- Original Message - 
From: 

To: 
Sent: Thursday, March 31, 2011 11:49 AM
Subject: gmx-users Digest, Vol 83, Issue 217



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Today's Topics:

  1. Heat of vap (Elisabeth)
  2. Re: Heat of vap (David van der Spoel)
  3. Re: Heat of vap (Justin A. Lemkul)
  4. Help on umbrella sampling (raghu...@bcpindia.org)
  5. Re: Help on umbrella sampling (Justin A. Lemkul)
  6. the total charge of system is not an integer (ahmet y?ld?r?m)


--

Message: 1
Date: Wed, 30 Mar 2011 15:22:56 -0400
From: Elisabeth 
Subject: [gmx-users] Heat of vap
To: Discussion list for GROMACS users 
Message-ID:

Content-Type: text/plain; charset="iso-8859-1"

Dear all,

I intend to obtain vaporization heat per volume for a *pure alkane 
system*.

Here is the steps I am taking. Please correct me.

1- Obtain total energy of system (kinetic+potential) and divide by number 
of
molecules to obtain energy per mol of molecules. g_energy -f *.edr -nmol 
XXX

2- Obtain total energy of a single molecule (use pbc).
3- Subtract step 2 from step 1.
4- Divide by simulation box volume.

My questions is:

in step 2 : what should be the box size? The same size as in 1 or it does
not matter? (step 1 is done for the actual denstiy)

Thanking you all,
Regards,
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Message: 2
Date: Wed, 30 Mar 2011 21:31:22 +0200
From: David van der Spoel 
Subject: Re: [gmx-users] Heat of vap
To: Discussion list for GROMACS users 
Message-ID: <4d93850a.3020...@xray.bmc.uu.se>
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On 2011-03-30 21.22, Elisabeth wrote:

Dear all,

I intend to obtain vaporization heat per volume for a /pure alkane
system/.  Here is the steps I am taking. Please correct me.

1- Obtain total energy of system (kinetic+potential) and divide by
number of molecules to obtain energy per mol of molecules. g_energy -f
*.edr -nmol XXX
2- Obtain total energy of a single molecule (use pbc).
3- Subtract step 2 from step 1.
4- Divide by simulation box volume.

My questions is:

in step 2 : what should be the box size? The same size as in 1 or it
does not matter? (step 1 is done for the actual denstiy)

do turn off all pbc and cutoff for that one.


Thanking you all,
Regards,




--
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205.
sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se


--

Message: 3
Date: Wed, 30 Mar 2011 15:30:12 -0400
From: "Justin A. Lemkul" 
Subject: Re: [gmx-users] Heat of vap
To: Discussion list for GROMACS users 
Message-ID: <4d9384c4.2040...@vt.edu>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed



Elisabeth wrote:

Dear all,

I intend to obtain vaporization heat per volume for a /pure alkane
system/.  Here is the steps I am taking. Please correct me.

1- Obtain total energy of system (kinetic+potential) and divide by
number of molecules to obtain energy per mol of molecules. g_energy -f
*.edr -nmol XXX
2- Obtain total energy of a single molecule (use pbc).
3- Subtract step 2 from step 1.
4- Divide by simulation box volume.

My questions is:

in step 2 : what should be the box size? The same size as in 1 or it
does not matter? (step 1 is done for the actual denstiy)



More troubling, how does one define the energy of a molecule?  If you use 
any
sort of long-range algorithms (especially PME, but also dispersion 
correction),

you can't simply decompose the system like this.

In the derivation of recent Gromos96 parameter sets, the heat of 
vaporization is

quite simple:

DHvap =  -  + RT

I have seen this equation used in a number of other studies, as well.

-Justin


Thanking you all,
Regards,



--


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




--

Message: 4
Date: Thu, 31 Mar 2011 02:14:50 +0530
From: raghu...@bcpindia.org
Subject: [gmx-users] Help on umbrella sampling
To: gmx-users@gromacs