[gmx-users] translation

priyanka srivastava priyankaps4 at yahoo.com
Mon Aug 11 22:32:57 CEST 2008 

You are right, I am using 3.3, sorry for this mistake. I will try the command which you have mentioned with -center zero for a small number of frames i.e. -b 2000 -e 3000 and get back to you. 

thnx,
Pri...



----- Original Message ----
From: Justin A. Lemkul <jalemkul at vt.edu>
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Sent: Tuesday, 12 August, 2008 1:15:00 AM
Subject: Re: [gmx-users] translation



priyanka srivastava wrote:
> Dear Justin,
> 
> Thanks a lot for replying back.
> 
> These are the two things that I have tried but still the peptide does 
> not come at the center:
> 
> 1. trjconv -f complete_production.xtc -s test.tpr -o test.pdb -center 
> zero -b 22000

The "-center zero" flag is not an option in 3.3.3, are you sure these are the 
commands you gave, and you are using the version you think you are?

I'm thinking that there is too big of a difference from 0 to 22 ns to allow 
trjconv accurately apply the fix.

Try this:

trjconv -f complete_production.xtc -s test.tpr -center

As a basic test, it should re-center your chosen group (Protein) every frame, 
allowing an iterative fix of the motion.

> Select group for centering
> Protein
> 
> Select group for output
> System
> 
> 2. trjconv -f complete_production.xtc -s test.tpr -center zero -fit 
> translation -b 22000 -o check2.pdb
> Select group for translational fit

Same comments as a above, if you don't process every frame (or at least a 
reasonably spaced subset), the algorithm doesn't tend to give the desired 
output, or so I have noticed with -center and -pbc options.

-Justin

> Selected 0: 'System'
> 
> Select group for centering
> Selected 1: 'Protein'
> 
> Select group for output
> System
> 
> I am using 3.3.3.
> 
> thnx,
> Priyanka..
> 
> 
> ----- Original Message ----
> From: Justin A. Lemkul <jalemkul at vt.edu>
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Sent: Tuesday, 12 August, 2008 12:05:26 AM
> Subject: Re: [gmx-users] translation
> 
> 
> 
> priyanka srivastava wrote:
>  > Dear All,
>  >
>  > I really apologize for asking a peptide translation related question
>  > again. I have a lipid-peptide system and I have already carried out the
>  > production run for 20ns. The peptide has moved towards one of the edges
>  > (I didnt specify comm-grps in the mdp file). I have to translate the
>  > peptide in the center of the bilayer. While using trjconv it translates
>  > the peptide at 0,0,0 but shifts the lipid and water molecules as well
>  > such that eventually the peptide lies near the edge only!
> 
> Without seeing what command you've actually tried, it's hard to make any
> recommendation.
> 
>  > Is there any other tool which I should be using?
> 
> trjconv is the tool you want, it's just a matter of finding the right 
> options.
> Under GMX 3.3.3, there is a -center flag that allows you to select a 
> group for
> centering.  In my protein/membrane systems, it has always worked well 
> (choose
> Protein for the group to be centered).
> 
> -Justin
> 
>  > Kindly suggest me something,
>  > Priyanka.
>  >
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> -- 
> ========================================
> 
> Justin A. Lemkul
> Graduate Research Assistant
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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-- 
========================================

Justin A. Lemkul
Graduate Research Assistant
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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