[gmx-users] Re:Re: how to calculate the non-bond interaction between solvent and solvent in pure solvent system (Justin A. Lemkul)
Justin A. Lemkul
jalemkul at vt.edu
Mon Oct 12 03:48:41 CEST 2009
Jinyao Wang wrote:
>> Jinyao Wang wrote:
>>> Hi gmx-users锛?
>>> I want to calculate the non-bond interaction (LJ+Coulomb) between solvent
>>> and solvent in pure solvent system. After the simulation of my pure
>>> solvent system, I calculated the interaction between solvent and solvent
>>> using the rerun option of the "mdrun program". First, I set the
>>> energygrps = sol sol in rerun.mdp file. Then, I make the grompp program
>>> like this, grompp -f rerun.mdp -c conf.gro -n index.ndx -p pure.top -o
>>> rerun.tpr But this step has a fatal error: Atom 1 in multiple energy Mon.
>>> groups (1 and 2)
>>> I don't know how to solve the problem and I want to know whether this
>>> method is effective for calculating the interaction between solvent and
>>> solvent in pure solvent system.
>>> Any suggestion will be appreciated.
>> These terms should already be present in the .edr file. Run g_energy and
>> have a look.
> Hi Justin, Thank you for your reply. But I still don't know how to set the
> "energygrps" option in the rerun.mdp for calculating the interaction between
> solvent molecule and solvent molecule in pure solvent system. As you said
> that these terms should be obtained running the g_energy,could you give me
> some details about the "energygrps" option in rerun.mdp file or how to
> calculate the intermolecular interaction in pure solvent system. Thanks in
If you have a pure solvent system, there is no way to set separate energygrps,
as you found out earlier. There is also no need to re-run your simulation. Use
g_energy to analyze your original ener.edr file; you will see the LJ and
Coulombic terms in the list of options.
> Jinyao Wang wangjy at ciac.jl.cn 2009-10-12
> _______________________________________________ gmx-users mailing list
> gmx-users at gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the www interface
> or send it to gmx-users-request at gromacs.org. Can't post? Read
Justin A. Lemkul
ICTAS Doctoral Scholar
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
More information about the gromacs.org_gmx-users