[gmx-users] xtc file

[Mark Abraham]

----- Original Message -----
From: "Justin A. Lemkul" <jalemkul at vt.edu>
Date: Sunday, May 23, 2010 13:49
Subject: Re: [gmx-users] xtc file
To: Discussion list for GROMACS users <gmx-users at gromacs.org>

> 
> 
> Moeed wrote:
> >Dear experts,
> >
> >I am trying to exclude all nonbonded interaction on hexane molecule.
> >
> >
> >1-For the md -rerun command I do not know how to get the input 
> XTC file. the program is expecting rerun.xtc
> >
> >mdrun -rerun -*x breakdown.xtc* -s Hexane-Stack125_md.tpr *-o 
> ORIGINAL-Trajectory-NOexcl.tpr* -c Hexane-Stack125_after_md -v 
> >& output.mdrun_m
> >
> 
> As I think I have said several times, you have to do this in 
> several steps. First, run a simulation using normal exclusions 
> that you believe to be valid by evaluating the properties of the 
> system.  If you set nstxtcout > 0 in your .mdp file, you 
> will get a .xtc trajectory file (.xtc output is off by default - 
> you must specify that you want it).  After you have done 
> this, use mdrun -rerun on this trajectory and whatever modified 
> topology you have created.

More precisely, mdrun -rerun will take any trajectory file, as can be seen by inspecting mdrun -h. There is no need to create an XTC file. There is a need to tell the previous mdrun to write positions when you want them to be available for the rerun, either with nstxout or nstxtcout.

> More specifically:
> 
> 1. mdrun -deffnm md_no_excl
> 2. grompp to create new .tpr file with special exclusions
> 3. mdrun -rerun md_no_excl.xtc -s md_with_new_excl.tpr
> 
> Thus, new energies will be calculated from a sensible trajectory.
> 
> >2-Can you please check exclsusions directive in top file. I 
> have used also nrexcl 5 in molecule top. does this make sense 
> given that I have defined all the possible exclusions in 19 lines.
> >
> 
> Much of what you have defined is redundant.  If you have 
> nrexcl = 5 that means nonbonded interactions between atoms up to 
> 5 bonds away are excluded already, so lines like "19 20" are 
> unnecessary.

Yep, use one approach or the other. Both won't hurt, but are redundant and error-prone.

Mark

> <snip>
> 
> All of the information I deleted is unnecessary.  I 
> appreciate that you are trying to be thorough, but long emails 
> with excess detail dilute the information that is really needed.
> 
> >[ moleculetype ]
> >; 
> Name            nrexcl
> >Hexane              5
> >
> 
> Not a bad approach, but...
> 
> >[ exclusions ]
> >1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20
> >2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20
> >3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20
> >4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20
> >5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20
> >6 7 8 9 10 11 12 13 14 15 16 17 18 19 20
> >7 8 9 10 11 12 13 14 15 16 17 18 19 20
> >8 9 10 11 12 13 14 15 16 17 18 19 20
> >9 10 11 12 13 14 15 16 17 18 19 20
> >10 11 12 13 14 15 16 17 18 19 20
> >11 12 13 14 15 16 17 18 19 20
> >12 13 14 15 16 17 18 19 20
> >13 14 15 16 17 18 19 20
> >14 15 16 17 18 19 20
> >15 16 17 18 19 20
> >16 17 18 19 20
> >17 18 19 20
> >18 19 20
> >19 20
> >
> 
> 
> ...why all the redundancy?  Much of what you have here is 
> already encompassed by the value of nrexcl.  Actually, if 
> you set nrexcl = 7, you don't have to create an [exclusions] 
> section at all!  There are no atoms more than 7 bonds away 
> from each other in hexane, right?
> 
> -Justin
> 
> -- 
> ========================================
> 
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> 
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