[gmx-users] Re:Re: how to calculate the non-bond interaction between solvent and solvent in pure solvent system (XAvier Periole)
Justin A. Lemkul
jalemkul at vt.edu
Mon Oct 12 04:12:39 CEST 2009
Jinyao Wang wrote:
>> From: XAvier Periole <x.periole at rug.nl> Subject: Re: [gmx-users] how to
>> calculate the non-bond interaction between solvent and solvent in pure
>> solvent system To: Discussion list for GROMACS users
>> <gmx-users at gromacs.org> Message-ID:
>> <BF11406F-B3B4-42E2-BCD0-011CE303F863 at rug.nl> Content-Type: text/plain;
>> charset=GB2312; format=flowed; delsp=yes
>>> 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)
>> This option can only calculate energies between non-overlapping groups.
>> That what he message is telling you: one atom can not be part of more than
>> one group.
>> If you actually have a simulation of pure solvent the total non-bonded
>> energy of your system seems to be what you are looking for!
> Hello XAvier. Thank you for your reply. Because I don't know how to set the
> option "energygrps" in rerun.mdp file, Now I still have no ideal for how to
> calculate the intermolecular interaction energy in pure solvent system.
This has already been explained in several posts, you are just asking the same
thing over and over. The energy contributions you are looking for are
calculated by default in MD, there is no need for special energygrps, and you do
not have to re-run your simulation. Analyze the original energy file with
g_energy, as I have said several times. Have you done this? You will clearly
see the energy terms you want.
> Could you give me some details. Thanks in advance for your suggestion.
> Jinyao Wang wangjy at ciac.jl.cn 2009-10-12
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Justin A. Lemkul
ICTAS Doctoral Scholar
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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