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.
Pooja 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 > 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.
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