[gmx-users] Fwd: query

[Nirali Desai]

Hello,

I want to calculate the energy of the two groups. I have defined those
groups in mdp file. I want to run it for 5 ns. So, I set the nsteps and all
parameters according to my need. Now I am using the rerun command for
calculating the energy. But it is only giving the energies till 100 ps and
not more than that. Please help me on this and guide me on  this problem.

using following commands:

1. Making index file according to the atoms: like a 1-15 PROA..etc like
for  PROB and PROC and then changing the energy groups in mdout.mdp file.
Any two groups at a time. (PROA, B,C= groups)
2. gmx grompp -f mdout.mdp -c nvt.gro -r nvt.gro -t nvt.cpt -p topol.top -n
index.ndx -o ie.tpr
3. gmx mdrun -deffnm -ie -rerun md.xtc
4. gmx energy -f ie.edr -s ie.tpr -o energy.xvg