On 2010-09-01 17.32, Sai Pooja wrote:
Hi,
Does gromacs allow the use of a _different set_ of energy tables for
different replicas? If not, any suggestions on how this can be done?
REM + 'different set of tables for each replica' + 'separate tables for
different pairs of energygroups'
Pooja
This would have to be programmed.
Note that in gromacs the coordinates (boxes) are exchanged, so the
temperatures are fixed on each node.
On Mon, Aug 30, 2010 at 7:25 PM, Mark Abraham <mark.abra...@anu.edu.au
<mailto:mark.abra...@anu.edu.au>> wrote:
----- Original Message -----
From: Sai Pooja <saipo...@gmail.com <mailto:saipo...@gmail.com>>
Date: Tuesday, August 31, 2010 2:45
Subject: Re: [gmx-users] LJ potential
To: Discussion list for GROMACS users <gmx-users@gromacs.org
<mailto:gmx-users@gromacs.org>>
>
> Thanks Mark. I have just 2 more queries regarding this.
>
*> When using tables for the potential, *
>
> 1) For VdW interactions, it it alright to use the topology
file generated by pdb2gmx using a forcefield (eg. CHARMM27) which
specifies LJ paramters as 'sigma' and 'epsilon' instead of C6 and
C12 as in the case of user defined potentials?
>
> I ask this because I get a warning when I try to do the above:
> :WARNING 2 [file initffd.top, line 8082]:
> Using sigma/epsilon based combination rules with user supplied
potential
> function may produce unwanted results
You will need to take suitable care. grompp will only use the
combination rules if it cannot find an existing definition for that
pair of atomtypes, so if you make all the definitions, you should be
OK. A good way to test that you are on the right track is whether
you can produce an energy group + table file that will reproduce the
result GROMACS gets if you leave it alone.
> 2) If one is interested in using PME for electrostatic
interactions but with different electrostatic interaction functions
for different pairs of energygrps, is it alright to specify the
simple coulomb function in the user defined table and use the
PME-User option for coulombtype?
Probably not. The form of the reciprocal-space PME term presupposes
a simple Coulomb function on all atoms. So did the parameterization
of the force field, so you're already taking your life in your hands :-)
Mark
> On Sun, Aug 29, 2010 at 7:54 PM, Mark Abraham
<mark.abra...@anu.edu.au> wrote:
>
>
> ----- Original Message -----
> From: Sai Pooja <saipo...@gmail.com>
> Date: Monday, August 30, 2010 3:33
> Subject: Re: [gmx-users] LJ potential
> To: Discussion list for GROMACS users <gmx-users@gromacs.org>
>
> > Hi,
> >
>
> > I am simulating a system of a protein in water. I am trying
to run the simulation with a modified protein-water LJ
and coulomb interaction. Since LJ and coulomb interaction
parameters are defined at the atomic level in the forcefield
files, I cannot figure out a good way to modify them for
protein-water interactions specifically. In other words, I want
to modify the protein water interaction without
altering protein-protein interaction.
>
> Right, that's totally different from your first question,
which implied only protein and thus intra-molecular
interactions. When seeking help, you should make sure you make
a complete description the first time, lest you waste
everybody's time and effort. That's easier said than done, but
you managed to do it on the second attempt :-)
>
> GROMACS allows you to use table lookups for non-bonded
interactions, and to use different tables for interactions
between different energy groups. So your problem reduces to
generating the different tables and groups, and assigning tables
to pairs of groups. Aspects of this process are discussed in
several places in the manual.
>
> Mark
>
>
> > On Tue, Aug 24, 2010 at 8:31 AM, Florian Dommert
<domm...@icp.uni-stuttgart.de> wrote:
> > -----BEGIN PGP SIGNED MESSAGE-----
> > Hash: SHA1
> >
> > On 08/24/2010 02:27 PM, Sai Pooja wrote:
> > > Hi,
> > >
> > > If there are n types of atoms in protein, how does
one specify:
> > > 1) Different types of LJ non-bonded interactions for
different pairs?
> > > 2) Modified Coloumb(by a pre-multiplier) interactions
for different pairs?
> > >
> > > Pooja
> > >
> > >
> >
> > Hi,
> >
> > this can be defined in the top file. Take a look at
the manual
> > regarding the force field and different function types
for the nonbonded
> > interactions. This will surely help.
> >
> > /Flo
> >
> > - --
> > Florian Dommert
> > Dipl.-Phys.
> >
> > Institute for Computational Physics
> >
> > University Stuttgart
> >
> > Pfaffenwaldring 27
> > 70569 Stuttgart
> >
> > Phone: +49(0)711/685-6-3613
> > Fax: +49-(0)711/685-6-3658
> >
> > EMail: domm...@icp.uni-stuttgart.de
> > Home: http://www.icp.uni-stuttgart.de/~icp/Florian_Dommert
> > -----BEGIN PGP SIGNATURE-----
> > Version: GnuPG v1.4.10 (GNU/Linux)
> > Comment: Using GnuPG with Mozilla -
http://enigmail.mozdev.org/
> >
> >
iEYEARECAAYFAkxzu7wACgkQLpNNBb9GiPlGAQCghZWQobj9j2SqvYC1gU5e3QR9
> > WVQAnAjv9tZ6xGRhc+S1vSSQh9kek4xZ
> > =T+Yb
> > -----END PGP SIGNATURE-----
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