On 5/12/13 1:31 PM, Hyunjin Kim wrote:
On 5/12/13 1:14 PM, Hyunjin Kim wrote:
On 5/12/13 12:54 PM, Hyunjin Kim wrote:
On 5/12/13 2:25 AM, Hyunjin Kim wrote:
Dear,
I want to calculate LJ and Electrostatic energies between two groups
defined in index.ndx during rerun with original trajectory.
The following is what I tried:
1. insert "energygrps r_1 r_25" in the test.mdp file.
2. grompp -f test.mdp -c x.gro -o x.tpr -p x.top -n index.ndx
3. mdrun -nt 2 -rerun o.trr -s x.tpr -o x.trr -c x.gro -g x.log -e
x.ene
The simulation runs properly, but if I collect energy using
g_energy,
then
values of all energy terms are same, although I choose different
groups.
Which specific groups did you choose?
Thanks a lot. I chose residues 1 and 25.
I understood that from the original post. What I was asking about was
the
exact
groups you chose from the g_energy selection menu.
When I use g_energy, I chose 4 5 6 7 8 9 10 from the below list. Thanks.
1 Bond 2 Angle 3 Ryckaert-Bell. 4 LJ-14
5 Coulomb-14 6 LJ-(SR) 7 Disper.-corr. 8
Coulomb-(SR)
9 Coul.-recip. 10 Potential 11 Kinetic-En. 12
Total-Energy
Dispersion correct, PME mesh (Coul-recip), and total potential are not
decomposable. The other terms you selected should be. The fact the these
options do not appear in the .edr file indicate either (1) you did not
rerun
with the right .tpr file or (2) you analyzed the wrong .edr file. The
approach
you have suggested is correct and should result in the desired energy
groups
being present. What version of Gromacs are you using?
I use 4.6.1 with gpu.
Are you doing the rerun on GPU, as well, or on CPU? What happens if you run in
serial (-nt 1)? I don't believe reruns work properly in parallel, but maybe
that's outdated information. Does a rerun on the .xtc file produce the desired
output?
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
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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