[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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> http://enigmail.mozdev.org/
> > >
> > >
> iEYEARECAAYFAkxzu7wACgkQLpNNBb9GiPlGAQCghZWQobj9j2SqvYC1gU5e3QR9
> > > WVQAnAjv9tZ6xGRhc+S1vSSQh9kek4xZ
> > > =T+Yb
> > > -----END PGP SIGNATURE-----
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--
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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