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?
-Justin
13 Temperature 14 Pres.-DC 15 Pressure 16 Box-X
17 Box-Y 18 Box-Z 19 Volume 20 Density
21 pV 22 Enthalpy 23 Vir-XX 24 Vir-XY
25 Vir-XZ 26 Vir-YX 27 Vir-YY 28 Vir-YZ
29 Vir-ZX 30 Vir-ZY 31 Vir-ZZ 32 Pres-XX
33 Pres-XY 34 Pres-XZ 35 Pres-YX 36 Pres-YY
37 Pres-YZ 38 Pres-ZX 39 Pres-ZY 40 Pres-ZZ
41 #Surf*SurfTen 42 Box-Vel-XX 43 Box-Vel-YY 44 Box-Vel-ZZ
45 T-System
In log file, "energygrp-flags[ 0]: 0".
I think this means it calculate system energies instead of two
specific
groups I choose.
Some energy terms are decomposable, most are not. There will be
obvious
differences in group names in the g_energy output.
I thought nonbonded energy terms were supposed to be decomposable, since
the two groups I selected are from one in solute and one in solvent. Am
I
wrong?
You will only get decomposed terms in the context of the interactions of
those
residues. Again, seeing the full g_energy selection menu would help us in
solving your problem. Thus far, I can see no evidence that Gromacs has
done
anything wrong, but I also haven't seen any diagnostic evidence of what
you have
tried to do. Please provide the details I have requested.
-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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--
========================================
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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