[gmx-users] Replica exchange with multiple tables?

Wed Sep 1 17:32:56 CEST 2010

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

On Mon, Aug 30, 2010 at 7:25 PM, Mark Abraham <mark.abraham at anu.edu.au>wrote:

>
>
> ----- Original Message -----
> From: Sai Pooja <saipooja at gmail.com>
> Date: Tuesday, August 31, 2010 2:45
> Subject: Re: [gmx-users] LJ potential
> To: Discussion list for GROMACS users <gmx-users at 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.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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> >
> >
> >
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-- 
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