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.abra...@anu.edu.au>wrote: > > > ----- Original Message ----- > From: Sai Pooja <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> > > > > > 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----- >>> > > -- >>> > > gmx-users mailing list gmx-users@gromacs.org >>> > > http://lists.gromacs.org/mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> >>> > > Please search the archive at http://www.gromacs.org/search before >>> posting! >>> > > Please don't post (un)subscribe requests to the list. Use the >>> > > www interface or send it to gmx-users-requ...@gromacs.org. >>> > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php >>> >> > > >> > > >> > > >> > > -- >> > > Quaerendo Invenietis-Seek and you shall discover. >> > > -- >> > > gmx-users mailing list gmx-users@gromacs.org >> > > http://lists.gromacs.org/mailman/listinfo/gmx-users >> > > Please search the archive at http://www.gromacs.org/search >> > > before posting! >> > > Please don't post (un)subscribe requests to the list. Use the >> > > www interface or send it to gmx-users-requ...@gromacs.org. >> > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php >> > >> > -- >> > gmx-users mailing list gmx-users@gromacs.org >> > http://lists.gromacs.org/mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> >> > Please search the archive at http://www.gromacs.org/search before >> posting! >> > Please don't post (un)subscribe requests to the list. Use the >> > www interface or send it to gmx-users-requ...@gromacs.org. >> > Can't post? Read http://www.gromacs.org/mailing_lists/users.php >> > > > > > > > > -- > > Quaerendo Invenietis-Seek and you shall discover. > > -- > > gmx-users mailing list gmx-users@gromacs.org > > http://lists.gromacs.org/mailman/listinfo/gmx-users > > Please search the archive at http://www.gromacs.org/search > > before posting! > > Please don't post (un)subscribe requests to the list. Use the > > www interface or send it to gmx-users-requ...@gromacs.org. > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- Quaerendo Invenietis-Seek and you shall discover.
-- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php