[gmx-users] xtc file

[Justin A. Lemkul]

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 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.

<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

-- 
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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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