[gmx-users] Exclude Coulomb interactions among certain atoms in SWM4 water molecule

[Justin Lemkul]

On 2/12/14, 12:52 AM, Sandipan Dutta wrote:
> Dear GMX users:
>
> I am fairly new to gromacs. I am trying to simulate SWM4 water model. In
> the model the electrostatic interactions between the Drude particle (DOH2)
> and oxygen atom (OP) are excluded. I have created an index file index.ndx
> that contains the numbers of the DOH2 and OP atoms. In the grompp.mdp file
> I have used the energygrp_excl command to exclude the energies between the
> groups. But when I run the grompp command:
>
> grompp -maxwarn 3 -n index.ndx
>
> I get the following error:
>
> WARNING 1 [file grompp.mdp]:
>    Can not exclude the lattice Coulomb energy between energy groups
>
> Fatal error:
> atoms 1 and 2 in charge group 1 of molecule type 'Other' are in different
> energy groups
>
> I have attached the grompp.mdp and the index.ndx files. Can someone please
> help me with these?
>

The attachments didn't survive.

Why do you need special index groups for doing this?  The Drude models should 
have a bond between DOH2 and OH2, and setting nrexcl to 2 will exclude these 
interactions.

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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