[gmx-users] Replica exchange with multiple tables?

David van der Spoel spoel at xray.bmc.uu.se
Wed Sep 1 17:38:53 CEST 2010


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.abraham at anu.edu.au
> <mailto:mark.abraham at anu.edu.au>> wrote:
>
>
>
>     ----- Original Message -----
>     From: Sai Pooja <saipooja at gmail.com <mailto: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
>     <mailto: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-----
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>              > > 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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>      >
>      >
>      >
>      > --
>      > Quaerendo Invenietis-Seek and you shall discover.
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> --
> Quaerendo Invenietis-Seek and you shall discover.
>


-- 
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205.
spoel at xray.bmc.uu.se    http://folding.bmc.uu.se



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