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

Justin Lemkul jalemkul at vt.edu
Fri Feb 21 14:05:58 CET 2014

On 2/21/14, 2:57 AM, Sandipan Dutta wrote:
> Dear GMX users:
> Thanks Justin for the reply. Yes there was a problem in the topology file .rtp.
> I am modifying the gmx.ff force field files. I have obtained swm4.itp from the
> gromacs link
> URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20110808/9d18f222/attachment.html>
>   Although I added the bond information in the ffbonded.itp file, I forgot to
> add the bond between the oxygen and the Drude particle in the .rtp file ( I
> followed the TIP4 water model which does not seem to have a bond with the IW
> particle and oxygen). But when I run the grompp I get an error
> ERROR 3 [file topol.top, line 48]:
>    No default Angle types
> This is because of the fact that I have not provided the angle between the Drude
> particle and the oxygen in the [ angletypes ] section of the ffbonded.itp file.
> I thought that since the bond length of Oxygen-Drude particle is zero we do not
> need the angle. How do I avoid mentioning the angle in ffbonded.itp?

There are no angle parameters involving Drudes or virtual sites.  In theory, 
since you've provided an angle type for it, there should be no problem, but the 
only defined angle should be H-O-H.



Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA 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


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