[gmx-users] LJ potential

[Sai Pooja]

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

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?
 Pooja


On Sun, Aug 29, 2010 at 7:54 PM, Mark Abraham <mark.abraham at anu.edu.au>wrote:

>
>
> ----- Original Message -----
> From: Sai Pooja <saipooja at gmail.com>
> Date: Monday, August 30, 2010 3:33
> Subject: Re: [gmx-users] LJ potential
> To: Discussion list for GROMACS users <gmx-users at 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 <
> dommert at 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: dommert at 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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> >
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