[gmx-users] x2top_d running for too long

[vivek sharma]

Hi All,
I am trying to generate the topology file for some molecule using x2top_d. I
have fired the command as:
*x2top_d -f Bromo-WR99210.pdb -o Bromo-WR99210.top -r Bromo-WR99210.rtp

*This is executing from last 16 hours, I dont know whether it takes this
much time or is there any problem with my run.

Can anybody give an idea of why the run is taking too long ?

With thanks,
Vivek
*
*
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Re: [gmx-users] x2top_d running for too long

[Mark Abraham]

vivek sharma wrote:

Hi All,
I am trying to generate the topology file for some molecule using 
x2top_d. I have fired the command as:

*/x2top_d -f Bromo-WR99210.pdb -o Bromo-WR99210.top -r Bromo-WR99210.rtp

/*This is executing from last 16 hours, I dont know whether it takes 
this much time or is there any problem with my run.


Can anybody give an idea of why the run is taking too long ?


Something is broken. There is no need to run x2top in double-precision, 
but this should not be the problem.


Mark
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RE: [gmx-users] units of eigenvalues of mass-weighted covariance matrix

[Berk Hess]

> Date: Wed, 10 Jun 2009 12:16:16 +1000
> From: mark.abra...@anu.edu.au
> To: gmx-users@gromacs.org
> Subject: Re: [gmx-users] units of eigenvalues of mass-weighted covariance 
> matrix
> 
> Wang Qin wrote:
> > Dear all,
> >  I am confused on the units of the eigenvalues calculated from 
> > g_covar of mass-weighted covariance matrix. From the output, it says the 
> > unit is  "(nm\S2\N)" but from my understanding, it is supposed to be kg/m2.
> 
> Various of the GROMACS analysis tools don't write the correct units in 
> .xvg output. This looks like such a case. There's a section early in the 
> manual that describes the GROMACS unit conventions, from which you
> should be able to deduce what the units are.
> 
> Mark

g_covar does write the correct units.
If your analysis would be mass weighted, it would have written (u nm\S2\N).
Apparently your output file is from a non mass-weighted analysis.
Note that by default the analysis is non mass weighted.

Berk


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RE: [gmx-users] Shell dynamics with vdW terms.

[Berk Hess]

> From: raf...@us.es
> To: gmx-users@gromacs.org
> Subject: Re: [gmx-users] Shell dynamics with vdW terms.
> Date: Wed, 10 Jun 2009 08:42:26 +0200
> 
> On Tuesday 09 June 2009 18:27:16 Berk Hess wrote:
> > > From: raf...@us.es
> > > To: gmx-users@gromacs.org
> > > Subject: Re: [gmx-users] Shell dynamics with vdW terms.
> > > Date: Tue, 9 Jun 2009 16:29:39 +0200
> > >
> > > On Tuesday 09 June 2009 10:02:47 Berk Hess wrote:
> > > > Hi,
> > > >
> > > > The equation you refer to is only an initial guess for the
> > > > optimization. The positions of the shells are optimized using the
> > > > forces from the full potential function.
> > > >
> > > > Berk
> > > >
> > > > > From: raf...@us.es
> > > > > To: gmx-users@gromacs.org
> > > > > Date: Tue, 9 Jun 2009 09:51:13 +0200
> > > > > Subject: [gmx-users] Shell dynamics with vdW terms.
> > > > >
> > > > > Hello,
> > > > >
> > > > > I have some troubles understanding the way used by Gromacs in
> > > > > optimizing the position of shells. In section 3.5.1 the manual says
> > > > > that the force on a shell particle is decomposed into two terms. The
> > > > > first represents the polarization and the second includes the Coulomb
> > > > > and van der Waals interactions. It continues assuming that the second
> > > > > term is constant and derives an analytic expression to calculate the
> > > > > shell position.
> > > > >
> > > > > My troubles arise after reading the paper: J. Phys. Chem. B 2009,
> > > > > 113, 7270-7281 by A. Villa, B. Hess & H. Saint-Martin. In the paper
> > > > > they simulate Lanthanides in water. In Table 2 they assign a 1/r**12
> > > > > term to the ion-shell - water-shell interaction (the A_MIM
> > > > > parameter). I believe that this term is used in eq. 8 of the
> > > > > Supporting Information. Because is vdW like it seems to me that it
> > > > > breaks the previously mentioned assumption of vdW constancy.
> > > > >
> > > > > Could anybody help me?
> > > > >
> > > > > Thanks a lot.
> > > > >
> > > > > Rafael
> > > > >
> > > > > --
> > > > > Dr. Rafael R. Pappalardo
> > > > > Dept. of Physical Chemistry, Univ. de Sevilla (Spain)
> > > > > e-mail: raf...@us.es
> > > > > ___
> > > > > gmx-users mailing listgmx-users@gromacs.org
> > > > > http://lists.gromacs.org/mailman/listinfo/gmx-users
> > > > > Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
> > > >
> > > > _
> > > > See all the ways you can stay connected to friends and family
> > > > http://www.microsoft.com/windows/windowslive/default.aspx
> > >
> > > Dear Berk,
> > >
> > > thanks for the quick answer.
> > >
> > > I am having lot of troubles trying to minimize a cation+1 water molecule
> > > using Gromacs 4.0.5. The minimization proceeds without warnings but at a
> > > certain point it seems that the shell minimizer does not work ok. The
> > > kind of structures I am obtaining are:
> > > Generated by trjconv : Cf in Water t=   9.0
> > > 6
> > > 1Cf_sCf1   1.49566   1.61167   1.73228
> > > 1Cf_sMs2   1.49450   1.62107   1.72892
> > > 2SOL OW3   1.51913   1.41088   1.80113
> > > 2SOLHW14   1.51596   1.36681   1.89843
> > > 2SOLHW25   1.53786   1.31814   1.75093
> > > 2SOL MW6   1.51789   1.42144   1.79730
> > >3.10740   3.10740   3.10740
> > > Generated by trjconv : Cf in Water t=  10.0
> > > 6
> > > 1Cf_sCf1   1.49838   1.58947   1.74003
> > > 1Cf_sMs2   1.49587   1.60861   1.73299
> > > 2SOL OW3   1.51772   1.42189   1.79765
> > > 2SOLHW14   1.51568   1.37036   1.89631
> > > 2SOLHW25   1.53733   1.32238   1.75035
> > > 2SOL MW6   1.51602   1.43730   1.79166
> > >3.10740   3.10740   3.10740
> > > Generated by trjconv : Cf in Water t=  11.0
> > > 6
> > > 1Cf_sCf1   1.50510   1.52690   1.75928
> > > 1Cf_sMs2   1.50102   1.57015   1.74742
> > > 2SOL OW3   1.51647   1.43148   1.79236
> > > 2SOLHW14   1.51461   1.38178   1.89116
> > > 2SOLHW25   1.53582   1.33543   1.74711
> > > 2SOL MW6   1.50797   1.50425   1.77168
> > >3.10740   3.10740   3.10740
> > >
> > > I see no warning or error in the md.log file albeit the Coulomb energy is
> > > rather large. The run continues at to t=50.000 with the message:
> > >
> > > Stepsize too small, or no change in energy.
> > > Converged to machine precision,
> > > but not to the requested precision Fmax < 0.1
> > >
> > > Could I sent you the input files in order to get some advice?
> > >
> > >
> > > Best regards,
> > >
> > > Rafael
> > >
> > > --
> > > Dr. Rafae

[gmx-users] Re: trouble for old/new GROMACS site

[Anna Marabotti]

Dear Justin,
thank you for the link you provided me, using it I'm able to find the gmx-user 
archive.

However, when I'm clicking directly on the link to the old GROMACS site 
provided in the new home page:
http://oldwww.gromacs.org the old home page opens with a series of warnings 
such as: "Warning: Cannot modify
header information - headers already sent by (output started at 
/data/gmx/www-gmx/configuration.php:75) in
/data/gmx/www-gmx/includes/joomla.php on line 697" at the top of the page. 

If, for example, I'm clicking the "Search" option, it points on the site:
http://oldwww.gromacs.org/component/option,com_wrapper/Itemid,165/ instead of 
the link you sent to me. The
appearance is similar to that of the new GROMACS site, and no content is 
present. How can I reach directly the
correct link?
On the contrary, if I click on the link provided for 
http://oldwiki.gromacs.org, all works fine.

I tried with bot Internet Explorer 8 and Mozilla Firefox 3.0.10, and the result 
is identical in both cases. I
don't know if this depends from settings of my PC, or of my firewall, security 
etc: the fact is that using the
links to the old GROMACS site, I cannot reach its content. I don't know if I'm 
the only person with this
difficulty, could you please check it?

Thanks anyway for the link and regards
Anna
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Re: [gmx-users] Re: trouble for old/new GROMACS site

[Mark Abraham]

Anna Marabotti wrote:

Dear Justin,
thank you for the link you provided me, using it I'm able to find the gmx-user 
archive.

However, when I'm clicking directly on the link to the old GROMACS site 
provided in the new home page:
http://oldwww.gromacs.org the old home page opens with a series of warnings such as: 
"Warning: Cannot modify
header information - headers already sent by (output started at 
/data/gmx/www-gmx/configuration.php:75) in
/data/gmx/www-gmx/includes/joomla.php on line 697" at the top of the page. 


If, for example, I'm clicking the "Search" option, it points on the site:
http://oldwww.gromacs.org/component/option,com_wrapper/Itemid,165/ instead of 
the link you sent to me. The
appearance is similar to that of the new GROMACS site, and no content is 
present. How can I reach directly the
correct link?
On the contrary, if I click on the link provided for 
http://oldwiki.gromacs.org, all works fine.

I tried with bot Internet Explorer 8 and Mozilla Firefox 3.0.10, and the result 
is identical in both cases. I
don't know if this depends from settings of my PC, or of my firewall, security 
etc: the fact is that using the
links to the old GROMACS site, I cannot reach its content. I don't know if I'm 
the only person with this
difficulty, could you please check it?


This sort of trouble will inevitably arise during and after a migration 
to a new server and/or software, whenever assumptions about the name of 
the host URL, or the services provided by it are violated. This would 
arise any time the old webpages had a hard reference to www.gromacs.org, 
since this likely to be invalid now. The general solution is to be 
patient until the transition is complete. Meantime, you can try using 
Google with a "site:oldwww.gromacs.org" constraint.


Mark
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Re: [gmx-users] x2top_d running for too long

[vivek sharma]

Hi Mark,
Thanks for your reply.
But I didn't got what does it mean?

2009/6/10 Mark Abraham 

> vivek sharma wrote:
>
>> Hi All,
>> I am trying to generate the topology file for some molecule using x2top_d.
>> I have fired the command as:
>> */x2top_d -f Bromo-WR99210.pdb -o Bromo-WR99210.top -r Bromo-WR99210.rtp
>>
>> /*This is executing from last 16 hours, I dont know whether it takes
>> this much time or is there any problem with my run.
>>
>> Can anybody give an idea of why the run is taking too long ?
>>
>
> Something is broken. There is no need to run x2top in double-precision, but
> this should not be the problem.
>

>
> Mark
> ___
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>
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Re: [gmx-users] x2top_d running for too long

[David van der Spoel]

vivek sharma wrote:

Hi Mark,
Thanks for your reply.
But I didn't got what does it mean?


It's a bug.

Please try one of the other programs from the download section on the 
website, e.g. topolbuild.


2009/6/10 Mark Abraham >


vivek sharma wrote:

Hi All,
I am trying to generate the topology file for some molecule
using x2top_d. I have fired the command as:
*/x2top_d -f Bromo-WR99210.pdb -o Bromo-WR99210.top -r
Bromo-WR99210.rtp

/*This is executing from last 16 hours, I dont know whether
it takes this much time or is there any problem with my run.

Can anybody give an idea of why the run is taking too long ?


Something is broken. There is no need to run x2top in
double-precision, but this should not be the problem. 




Mark
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--
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Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205. Fax: +4618511755.
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[gmx-users] problem in running grompp

[Samik Bhattacharya]

hi, i am simulating a membrane protein inside dppc bilayer and in this regard i 
am following justin's tutorial. but i ma facing a problem in running 
grompp...whenever i run it is giving error 

Program grompp, VERSION 4.0.5
Source code file: grompp.c, line: 362

Fatal error:
number of coordinates in coordinate file (1A68_genbox.gro, 49128)
 does not match topology (1A68.top, 48628)

now how to solve this problem? i have first generated the lipid box  with the 
protein then solvated it. i really need little bit of help to proceed to the 
next step...
Thaking You...
Shamik





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[gmx-users] Re: problem in running grompp

[Justin A. Lemkul]

Samik Bhattacharya wrote:
hi, i am simulating a membrane protein inside dppc bilayer and in this 
regard i am following justin's tutorial. but i ma facing a problem in 
running grompp...whenever i run it is giving error


Program grompp, VERSION 4.0.5
Source code file: grompp.c, line: 362

Fatal error:
number of coordinates in coordinate file (1A68_genbox.gro, 49128)
 does not match topology (1A68.top, 48628)

now how to solve this problem? i have first generated the lipid box  
with the protein then solvated it. i really need little bit of help to 
proceed to the next step...


The answer to this question is always the same.  You did not correctly update 
your topology after some preparation step.  You are off by 500 atoms, which, if 
you are using DPPC like the tutorial, corresponds to 10 lipids.  Look at what 
you've done carefully.


-Justin


Thaking You...
Shamik




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Ph.D. Candidate
ICTAS Doctoral Scholar
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] vdwradii.dat - where do the values come from?

[João M . Damas]

Hi there GMX users,

Does anyone know where do the van der waals radii values that are in the
vdwradii.dat come from? I've searched the archives and David said once that
he didn't recall where they were token from. If there is no information
whatsoever of where do they come from and since it would be difficult to
introduce other element's van der waals radii consistent to the current
ones, why keep using them?

Regards,
João

-- 
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PhD Student
Protein Modelling Group
ITQB-UNL, Oeiras, Portugal
Tel:+351-214469613
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[gmx-users] problem fitting trajectory

[Rebeca García Fandiño]

Hello,
I have done a simulation using Gromacs 4 (4.0.2) and I would like to have a 
trajectory were the protein is fitted to the first structure (to mantain the 
exact orientation).

When I have tried

echo 1 1 0 | trjconv -f production_1_3.xtc -s production1.tpr -center -fit 
rot+trans -pbc mol -o production_1_3_fit.xtc

visualizing production_1_3_fit.xtc I can see that the protein is fitted, 
however there are a lot of "holes" into the water box. It seems like the pbc 
were not correctly applied. I have tried changing a lot of options (-pbc res, 
-boxcenter rect,...) but nothing works.

The options

trjconv -f production_1_3.xtc -s production1.tpr -center -boxcenter rect -fit 
rot+trans -pbc mol -o production_1_3_fit.xtc

do not produce any hole in the box of water, but the box entirely moves around 
the protein, and sometimes it is outside of it and not solvated.

I have also tried using Gromacs 4.0.4, but the problem is still the same.

Could anybody give an idea of how solving it, please?

Thank you very much for your help.

Best wishes,

Rebeca Garcia 
Academic Visitor
Oxford University

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Re: [gmx-users] problem fitting trajectory

[Justin A. Lemkul]

I have found that the combination of -pbc mol -ur compact always looks pretty :) 
 So in addition to -fit and perhaps -center, try those two options together.


-Justin

Rebeca García Fandiño wrote:

Hello,
I have done a simulation using Gromacs 4 (4.0.2) and I would like to 
have a trajectory were the protein is fitted to the first structure (to 
mantain the exact orientation).


When I have tried

echo 1 1 0 | trjconv -f production_1_3.xtc -s production1.tpr -center 
-fit rot+trans -pbc mol -o production_1_3_fit.xtc


visualizing production_1_3_fit.xtc I can see that the protein is fitted, 
however there are a lot of "holes" into the water box. It seems like the 
pbc were not correctly applied. I have tried changing a lot of options 
(-pbc res, -boxcenter rect,...) but nothing works.


The options

trjconv -f production_1_3.xtc -s production1.tpr -center -boxcenter rect 
-fit rot+trans -pbc mol -o production_1_3_fit.xtc


do not produce any hole in the box of water, but the box entirely moves 
around the protein, and sometimes it is outside of it and not solvated.


I have also tried using Gromacs 4.0.4, but the problem is still the same.

Could anybody give an idea of how solving it, please?

Thank you very much for your help.

Best wishes,

Rebeca Garcia
Academic Visitor
Oxford University


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--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
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] Small molecule-protein complexes MD simulations

[Andrew Voronkov]

This is of course the question which was discussed many times, but I just  want 
to ask about updates for it.
Is there any port for GAFF force field now? Is it possible to prepare small 
molecule ligands for GROMACs MD with Amber force fields without Amber version 
installed?

Best regards,
Andrew
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Re: [gmx-users] problem fitting trajectory

[Tsjerk Wassenaar]

Hi,

It is better to do PBC options first and fitting options after, with
separate calls to trjconv. Fitting and PBC don't go well together,
This has been elaborately discussed on the mailing list before.

Cheers,

Tsjerk

On Wed, Jun 10, 2009 at 8:59 PM, Justin A. Lemkul wrote:
>
> I have found that the combination of -pbc mol -ur compact always looks
> pretty :)  So in addition to -fit and perhaps -center, try those two options
> together.
>
> -Justin
>
> Rebeca García Fandiño wrote:
>>
>> Hello,
>> I have done a simulation using Gromacs 4 (4.0.2) and I would like to have
>> a trajectory were the protein is fitted to the first structure (to mantain
>> the exact orientation).
>>
>> When I have tried
>>
>> echo 1 1 0 | trjconv -f production_1_3.xtc -s production1.tpr -center -fit
>> rot+trans -pbc mol -o production_1_3_fit.xtc
>>
>> visualizing production_1_3_fit.xtc I can see that the protein is fitted,
>> however there are a lot of "holes" into the water box. It seems like the pbc
>> were not correctly applied. I have tried changing a lot of options (-pbc
>> res, -boxcenter rect,...) but nothing works.
>>
>> The options
>>
>> trjconv -f production_1_3.xtc -s production1.tpr -center -boxcenter rect
>> -fit rot+trans -pbc mol -o production_1_3_fit.xtc
>>
>> do not produce any hole in the box of water, but the box entirely moves
>> around the protein, and sometimes it is outside of it and not solvated.
>>
>> I have also tried using Gromacs 4.0.4, but the problem is still the same.
>>
>> Could anybody give an idea of how solving it, please?
>>
>> Thank you very much for your help.
>>
>> Best wishes,
>>
>> Rebeca Garcia
>> Academic Visitor
>> Oxford University
>>
>> 
>> Charlas más divertidas con el nuevo Windows Live Messenger
>> 
>>
>>
>> 
>>
>> ___
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>
> --
> 
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> 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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-- 
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623
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Re: [gmx-users] Small molecule-protein complexes MD simulations

[Mark Abraham]

Andrew Voronkov wrote:

This is of course the question which was discussed many times, but I just  want 
to ask about updates for it.
Is there any port for GAFF force field now? Is it possible to prepare small 
molecule ligands for GROMACs MD with Amber force fields without Amber version 
installed?


The AMBER tools package is designed to meet this kind of need, I 
understand. See their website.


Mark
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[gmx-users] g_energy returns the instantaneous data or the average data?

[Chih-Ying Lin]

Hi
I want to calculate the pressure and the energy for the system.


my .mdp file is as follows; writing out the energy and coordinates per
1000 steps.
nstenergy = 1000   ; Writing out energy information every step
nstxtcout = 1000   ; Writing coordinates every step


After entering g_energy command,
the pressure and the energy are calculated.

Are the pressure and the energy calculated for the instantanous
pressure and energy
on the time point of the 1000th, 2000th ... time step ?

Or, the pressure and the energy are averagely calculated over the time
period 0-1000, 1001-2000.time steps?

Which one is true?

Thank you
Lin
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Re: [gmx-users] g_energy returns the instantaneous data or the average data?

[Mark Abraham]

Chih-Ying Lin wrote:



Hi
I want to calculate the pressure and the energy for the system.


my .mdp file is as follows; writing out the energy and coordinates per 1000 
steps.

nstenergy = 1000   ; Writing out energy information every step
nstxtcout = 1000   ; Writing coordinates every step


After entering g_energy command,
the pressure and the energy are calculated.

Are the pressure and the energy calculated for the instantanous pressure and energy 


on the time point of the 1000th, 2000th ... time step ?

Or, the pressure and the energy are averagely calculated over the time period 0-1000, 1001-2000.time steps? 


Which one is true?


Both. See Appendix C.

Mark
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Re: [gmx-users] problem fitting trajectory

[Daniel Adriano Silva M]

Hi,
This is a recurrent issue. I have figured a bash script that had
worked for every system which I had tested (i.e. protein,
protein-ligand, protein-DNA, protein-protein), but this is not a
warranty. It centers the protein on the box, and at the same time puts
waters inside the box ; however the apparent effect is that the water
box moves around "a center".
Test it, and please advice if it does the work and/or comment (maybe
developers could integrate a similar filter in a future gmx_trjconv
release, or just publish something similar to this in the wiki).

Best.
Daniel

***
Usage notes:

- Just copy/and/paste the code on a textfile and make it executable
with "chmod 700", !!!take care of broken/split lines by email/post
artifacts!!!
- I use mdrun with -deffnm for the outputs; therefore this script is
made to work when all the output files have the same name.
- Do not forget to replace the *** field for the GROBIN variable on the code.
- On the code 0 and 1 are the index groups for system and protein
respectively. However, for any complex the trick to have a nice
representation is to center the system only on one of the proteins,
for example, for me:
  echo -e "del 1-14\n r 1-238\n r 1-239\n q\n" |
$GROBIN/make_ndx -f pre1_$NAME.gro -o pre1_$NAME.ndx
makes the trick, since it erases all the groups from my index, except
system, and then creates the group 1 only for one of my proteins
(residues 1-238) and additionally the group 2 used to output  my
complex in the absence of waters (residues 1-239).

To run use:
  ./scriptname
PATH-TO-DINAMIC/MDOUTPUT-NAME-WITHOUT-DOT-OR-EXTENSIONS  OUTPUT-NAME
Example:
  ./filterscript  /home/dsilva/dynamic/production/md  filteredmd

***
CODE:
***


#!/bin/bash
#Daniel Silva, script to filter trajectories
PATH=$1
NAME=$2
GROBIN=/usr/local/gromacs/bin   #MODIFY THIS LINE TO POINT TO
YOUR GROMACS BINARIES PATH
/bin/cp $PATH.tpr ./$NAME-filtered.tpr
echo -e "0\n"| $GROBIN/trjconv -f $PATH -s
$NAME-filtered.tpr -pbc whole  -o pre1_$NAME
echo -e "0\n"| $GROBIN/trjconv -f $PATH -s
$NAME-filtered.tpr -pbc whole  -o pre1_$NAME.gro -e 0
### Modify the next line if you have any kind of complex, in order to
make group 1 pointing only to one of proteins in the complex.
(Example: echo -e "del 1-14\n r 1-238\n r 1-239\n q\n" |
$GROBIN/make_ndx -f pre1_$NAME.gro -o pre1_$NAME.ndx)
echo -e "q\n" | $GROBIN/make_ndx -f pre1_$NAME.gro -o pre1_$NAME.ndx
echo -e "1\n0\n" | $GROBIN/trjconv -f pre1_$NAME -s
$NAME-filtered.tpr -pbc atom -ur compact -center -n pre1_$NAME.ndx -o
pre2_$NAME
echo -e "1\n0\n" | $GROBIN/trjconv -f pre2_$NAME -s
$NAME-filtered.tpr -fit rot+trans -n pre1_$NAME.ndx -o $NAME-filtered
echo -e "0\n"| $GROBIN/trjconv -f $NAME-filtered -s
$NAME-filtered.tpr -e 0 -n pre1_$NAME.ndx -o $NAME-filtered.gro
### If you also want to output trajectories without waters uncomment
the next two lines. Also, if you have complexes take care of the group
that you are sending to the output (Example, for me it needs to be
group 2 not 1; echo -e "1\n2\n" and echo -e "2\n", respectively for
the next two lines)
#   echo -e "1\n1\n" | $GROBIN/trjconv -f pre2_$NAME -s
$NAME-filtered.tpr -fit rot+trans -n pre1_$NAME.ndx -o
$NAME-filtered-NoHOH
#   echo -e "1\n"| $GROBIN/trjconv -f $NAME-filtered -s
$NAME-filtered.tpr -e 0 -n pre1_$NAME.ndx -o $NAME-filtered-NoHOH.gro
/bin/rm ./pre*_$NAME.*



###CODE END






2009/6/10 Tsjerk Wassenaar :
> Hi,
>
> It is better to do PBC options first and fitting options after, with
> separate calls to trjconv. Fitting and PBC don't go well together,
> This has been elaborately discussed on the mailing list before.
>
> Cheers,
>
> Tsjerk
>
> On Wed, Jun 10, 2009 at 8:59 PM, Justin A. Lemkul wrote:
>>
>> I have found that the combination of -pbc mol -ur compact always looks
>> pretty :)  So in addition to -fit and perhaps -center, try those two options
>> together.
>>
>> -Justin
>>
>> Rebeca García Fandiño wrote:
>>>
>>> Hello,
>>> I have done a simulation using Gromacs 4 (4.0.2) and I would like to have
>>> a trajectory were the protein is fitted to the first structure (to mantain
>>> the exact orientation).
>>>
>>> When I have tried
>>>
>>> echo 1 1 0 | trjconv -f production_1_3.xtc -s production1.tpr -center -fit
>>> rot+trans -pbc mol -o production_1_3_fit.xtc
>>>
>>> visualizing production_1_3_fit.xtc I can see that the protein is fitted,
>>> however there are a lot of "holes" into the water box. It seems like the pbc
>>> were not correctly applied. I have tried changing a lot of options (-pbc
>>> res, -boxcenter rect,...) but nothing works.
>>>
>>> The options
>>>
>>> trjconv -f production_1_3.xtc -s production1.tpr -center -boxcenter rect
>>> -fit rot+trans -pbc mol -o production_1_3_fit.xtc
>>>
>>> do not produce any hole in the box of water, but the box entirely moves
>>> around 

[gmx-users] problem regarding removal of water from final simulation system.

[nitu sharma]

Dear all

 I have done successfully simulation of membrane protein , but after that to
visualise my final model clearly I have to remove water molecules from my
system (protein+lipid+water).

But  I have no Idea about the which command I should use to do this even it
doesn't mentioned in justin,s tutorial also to make final pdb after
simulation.

So can anyone suggest me  how to remove water form my final simulation
system to make final pdb of only protein and lipid molecule?

If anyone can help me I willbe really thankful for him/her.

Nitu Sharma.
Jawaherlal Nehru University
New Delhi , India.
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RE: [gmx-users] problem regarding removal of water from final simulation system.

[Dallas B. Warren]

Two ways:

 

1 - turn them off with the visualisation software you are using, only
display the protein and lipid

2 - use editconf and the appropriate index groups

 

Catch ya,

Dr. Dallas Warren
Department of Pharmaceutical Biology and Pharmacology
Pharmacy and Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3010
dallas.war...@pharm.monash.edu.au
+61 3 9903 9167
-
When the only tool you own is a hammer, every problem begins to resemble
a nail. 

From: gmx-users-boun...@gromacs.org
[mailto:gmx-users-boun...@gromacs.org] On Behalf Of nitu sharma
Sent: Thursday, 11 June 2009 3:19 PM
To: gmx-users@gromacs.org
Subject: [gmx-users] problem regarding removal of water from final
simulation system.

 

Dear all 

 I have done successfully simulation of membrane protein , but after
that to visualise my final model clearly I have to remove water
molecules from my system (protein+lipid+water).

But  I have no Idea about the which command I should use to do this even
it doesn't mentioned in justin,s tutorial also to make final pdb after
simulation.

So can anyone suggest me  how to remove water form my final simulation
system to make final pdb of only protein and lipid molecule?

If anyone can help me I willbe really thankful for him/her.

Nitu Sharma.
Jawaherlal Nehru University
New Delhi , India.

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Re: [gmx-users] problem regarding removal of water from final simulation system.

[Mark Abraham]

nitu sharma wrote:

Dear all

 I have done successfully simulation of membrane protein , but after 
that to visualise my final model clearly I have to remove water 
molecules from my system (protein+lipid+water).


But  I have no Idea about the which command I should use to do this even 
it doesn't mentioned in justin,s tutorial also to make final pdb after 
simulation.


So can anyone suggest me  how to remove water form my final simulation 
system to make final pdb of only protein and lipid molecule?


You asked a very similar question a few days ago, which I answered then. 
http://oldwww.gromacs.org/pipermail/gmx-users/2009-June/042525.html You 
want to extract a non-standard group (i.e. non-solvent), so you need to 
make an index file that defines that group.


Mark
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[gmx-users] gromacs-4.0.5 parallel run in 8 cpu: slow speed

[Thamu]

>
> Hi
>
> Recently I successfully installed the gromacs-4.0.5 mpi version.
> I could run in 8 cpu. but the speed is very slow.
> Total number of atoms in the system is 78424.
> while running all 8 cpu showing 95-100% CPU.
>
> How to speed up the calculation.
>
> Thanks
>
>
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Re: [gmx-users] gromacs-4.0.5 parallel run in 8 cpu: slow speed

[Jussi Lehtola]

On Thu, 2009-06-11 at 14:35 +0800, Thamu wrote:
> Hi
> 
> Recently I successfully installed the gromacs-4.0.5 mpi
> version.
> I could run in 8 cpu. but the speed is very slow. 
> Total number of atoms in the system is 78424.
> while running all 8 cpu showing 95-100% CPU.

That's normal for a system that atoms/cpu ratio.
What's your system and what mdp file are you using?
-- 
--
Jussi Lehtola, FM, Tohtorikoulutettava
Fysiikan laitos, Helsingin Yliopisto
jussi.leht...@helsinki.fi, p. 191 50632
--
Mr. Jussi Lehtola, M. Sc., Doctoral Student
Department of Physics, University of Helsinki, Finland
jussi.leht...@helsinki.fi
--


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Re: [gmx-users] gromacs-4.0.5 parallel run in 8 cpu: slow speed

[Mark Abraham]

Thamu wrote:

Hi

Recently I successfully installed the gromacs-4.0.5 mpi version.


Possibly.


I could run in 8 cpu. but the speed is very slow.
Total number of atoms in the system is 78424.
while running all 8 cpu showing 95-100% CPU.

How to speed up the calculation.


You haven't given us any diagnostic information. The problem could be 
that you're not running an MPI GROMACS (show us your configure line, 
your mdrun command line and the top 50 lines of your .log file).


Mark
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