If you want to keep any group planar during MD you can try to define improper
dihedrals in your topology file.
See the manual, ff*.rtp and ff*bon.itp files.
-Original Message-
From: Abu Naser <[EMAIL PROTECTED]>
To:
Date: Thu, 26 Jun 2008 15:46:36 +
Subject: [gmx-users] keeping 4 ato
Now you have a charge there and no mass. Thats, how virtual sites work.
> If you want to use a "free energy dummy", you may have to use a
> different approach.
>
> Regards
>
> Maik Goette, Dipl. Biol.
>
> Нилов Дмитрий wrote:
> > I`ve tried to name it like at
rror
"virtual site D (Res FMT-1) has non-zero mass 12.011".
I suppose, that only "dummy masses"(particles named like "M*") could
have mass.
Could you help me, please?
Nilov Dmitri
-Original Message-
> Нилов Дмитрий wrote:
> > OK,
al sites
> > ERROR 2 [file "fmt.top", line 82]:
> > virtual site C (Res FMT-1) has non-zero mass 12.011
> > -
> >
> > -Original Message-
> >> Нилов Дмитрий wrote:
> >>> Hello!
>
From: David van der Spoel <[EMAIL PROTECTED]>
To: Discussion list for GROMACS users
Date: Sat, 19 Jan 2008 10:33:50 +0100
Subject: Re: [gmx-users] Virtual site and constraints
>
> Нилов Дмитрий wrote:
> > Hello!
> > I would like to involve formate molecule (HCOO-)in my
Hello!
I would like to involve formate molecule (HCOO-)in my dynamics, but I have the
problem when I use virtual site (type 3fd)for it.
When I run grompp for single formate molecule, it`s ok.
But after solvating in bath of solvent (tip3p) grompp runs with error:
Cleaning up constraints and const
Hello!
I would like to involve formate molecule (HCOO-)in my dynamics, but I have the
problem when I use virtual site (type 3fd)for it.
When I run grompp for single formate molecule, it`s ok.
But after solvating in bath of solvent (tip3p) grompp runs with error:
Cleaning up constraints and const
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