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
--
========================================
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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