I'm trying to simulate three alpha spectrin repeats (R15, R16, R17) using a structure based C-alpha model: http://smog.ucsd.edu/. My task is first to modify the sample .mdp file available at http://smog.ucsd.edu/GromacsTutorial.html. I'm having some difficulty figuring out what to set rlist, rcoulomb and rvdw to. I don't think I need to change anything else except for trying different temperatures? My simulation is running now, but I don't think it's running correctly. I set these parameters somewhat arbitrarily, mainly based on the errors I was getting.
After I get that working, I'd like to somehow provide gromacs with a table that tells it the native interaction energies between different pairs of residues (e.g. ALA & GLN) so that it doesn't assign a generic interaction energy value to all native interactions. (I think it's doing that now.) I'm a complete newb to gromacs, sorry! I read through most of the manual, but I'm still confused about many of these parameters. I'd really appreciate it if you could help me. Gene On 2010-05-21, at 5:33 PM, Mark Abraham wrote: > ----- Original Message ----- > From: Gene Polovy <gpol...@gmail.com> > Date: Saturday, May 22, 2010 8:37 > Subject: [gmx-users] specifying interaction energy between residues > To: gmx-users@gromacs.org > >> Hi There, >> >> I'm trying to run a course grained (c alpha) simulation of a > > Letting us know more about what kind of coarse-grained model you're trying to > modify would be useful. > >> protein and I'd like to know how/where I can define >> heterogeneous native interaction energies between residues. Is >> it under [ pairs ] in the topology file? In other words, I'd >> like to use a flavored model rather than a vanilla model. Please help! > > Ah, but we're not sure what your vanilla model is, so it's hard to advise... > > Mark > -- > 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
