[gmx-users] questions related to genpairs=no

Yang Ye leafyoung81-group at yahoo.com
Wed Feb 15 02:02:37 CET 2006

Note that 3.3 has serious problem with LJ in comb-rule 3. They will treat as
the same as comb-rule 1 which results in near zero values for sigma and
epsilon. Use gmxdump to check the tpr generated. Use previous version
(3.2.1) 's grompp instead.

Yang Ye

> -----Original Message-----
> From: gmx-users-bounces at gromacs.org [mailto:gmx-users-bounces at gromacs.org]
> On Behalf Of Berk Hess
> Sent: Tuesday, February 14, 2006 7:35 PM
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] questions related to genpairs=no
> >From: David van der Spoel <spoel at xray.bmc.uu.se>
> >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] questions related to genpairs=no
> >Date: Tue, 14 Feb 2006 08:54:36 +0100
> >
> >Wusheng Zhu wrote:
> >>Dear All,
> >>I am trying to set combination rule =3 and genpairs=no in the [default]
> >>part. I have two questions:
> >>(1) when I listed explicit [pairtypes] or [pairs], what parameters
> should
> >>follow each pairs atomA-atomB ? Are they simply epsilon_AB and sigma_AB
> >>calculated by combination rule, or should one of they be scaled
> >>multiplying with Fudge factors such as epsilon_AB*FudgeLJ and the other
> >>one simply be sigma_AB?
> >>(2) Where to define FudgeQQ for 1-4 pairs Coulomb interaction as there
> are
> >>only two LJ parameters V,W (epsilon, sigma) following the pairs list
> based
> >>on the manual? So basically, how to put FugeLJ and FugeQQ into the
> >>topology file when genpairs=no?
> >
> >First of all you can check the result in the tpr file by using
> >gmxdump -s topol.tpr | less
> >and search for LJ14.
> >
> >In the pairtypes or pairs section you probably can not give sigma and
> >epsilon but have to compute the C6 and C12 directly. Please check using
> the
> >above method.
> In Gromacs 3.3 you should give sigma and epsilon when using combination
> rule
> 3.
> >
> >You only need to specify pairtypes if they are different than what would
> be
> >generated. FudgeLJ is *only* used with genpairs = no, otherwise you have
> >full LJ interactions. FudgeLJ will modify the C12 and C6 params directly
> in
> >the tpr file. FudgeQQ is used for 1-4 Coulomb interactions if you specify
> >it in the topology. You will find the number back in the parameter
> section
> >of the tpr file (and md.log file).
> No.
> FudgeLJ is *only* used with genpairs=yes.
> And then only for pairs that are not listed in the pairstypes section,
> i.e. those that are really generated from the normal non-bonded
> Berk.
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