[gmx-developers] Re: gmx-developers Digest, Vol 12, Issue 4

Michael Shirts mrshirts at gmail.com
Tue Apr 19 14:43:09 CEST 2005

Ah, I was having problems with [ pairs ], too.  Good to know.

What's the current plans for the 3.3 release?  I'm anxious to get
going on some edits and (hopefully!) improvements on the next version
. . .


> Date: Mon, 18 Apr 2005 16:43:29 -0600
> From: Walter Ash <wlash at ucalgary.ca>
> Subject: [gmx-developers] Possible bug in grompp?
> To: gmx-developers at gromacs.org
> Message-ID: <42643811.9010709 at ucalgary.ca>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
> I've been working on a new molecule topology and I've noticed what I
> believe is a bug in grompp...  I am using the ffopls forcefield with
> genpairs=yes, fudgeQQ and fudgeLJ = 0.5,  and combination rule 3.  This
> is with the 3.2.1 distribution version.
> In the molecular topology, under [ pairs ], it appears I have to specify
> LJ14 parameters in C6 and C12 format despite the use of sigma and
> epsilon everywhere else in this forcefield (comb rule 3).  If I use
> sigma and epsilon in a [ pairs ] definition, my LJ14 energies are orders
> of magnitude too high as grompp intereprets these parameters as C6 and
> C12 values instead.  Putting C6 and C12 parameters here gives the
> expected behavior.
> This is contrary to what is stated in the manual and what I would expect
> the behavior to be.

More information about the gromacs.org_gmx-developers mailing list