[gmx-users] cgnr

Berk Hess gmx3 at hotmail.com
Fri May 5 14:28:13 CEST 2006

>From: "Marcelo A. Carignano" <cari at purdue.edu>
>Reply-To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>To: "'Discussion list for GROMACS users'" <gmx-users at gromacs.org>
>Subject: RE: [gmx-users] cgnr
>Date: Thu, 4 May 2006 16:35:29 -0400
>Done. Posted bug # 75.
>I hope my explanation is clear.
>-----Original Message-----
>From: gmx-users-bounces at gromacs.org [mailto:gmx-users-bounces at gromacs.org]
>On Behalf Of David van der Spoel
>Sent: Thursday, May 04, 2006 4:05 PM
>To: Discussion list for GROMACS users
>Subject: Re: [gmx-users] cgnr
>Marcelo A. Carignano wrote:
> > Cutoff I set at 3.00 nm
> > The distance between the two molecules is about 0.1 nm.
> > The box is a cube of 20 nm
> >
> > A bug perhaps?
>Could be, please submit a bugzilla.

The problem is that NH3 all one charge group
is recognized as TIP4P water and therefore optimized,
while the N does have charge and the waterloops
assume it does not.

The solvent check in mdrun should check for 0 charge
of the first atom for tip4p optimization.


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