[gmx-users] question about energygrps
hyunjink at andrew.cmu.edu
Sun May 12 19:14:01 CEST 2013
> On 5/12/13 12:54 PM, Hyunjin Kim wrote:
>>> On 5/12/13 2:25 AM, Hyunjin Kim wrote:
>>>> 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
>>>> The simulation runs properly, but if I collect energy using g_energy,
>>>> values of all energy terms are same, although I choose different
>>> 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
> 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
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
>>>> In log file, "energygrp-flags[ 0]: 0".
>>>> I think this means it calculate system energies instead of two
>>>> groups I choose.
>>> Some energy terms are decomposable, most are not. There will be
>>> 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
> You will only get decomposed terms in the context of the interactions of
> 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
> 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 A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
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