Dear users, I have a dimeric protein system, where I would like to define two pairwise sidechain-sidechain distances, one in each monomer. I'd like to do this back and forth, so that I can alternately enforce long (~0.6nm) and short (~0.3nm) distances, and follow the response of the protein. I have reason to believe that this will be meaningful.
I'm running with "constraints = all-bonds", and so introducing new bonds or constraints causes LINCS-related crashes. I then have to minimize and equilibrate between runs, and this would make the above "experiment" less easy to interpret. I would really like to use the pull code to apply a harmonic potential on top of all the constraints, but as I understand it that doesn't allow defining two distances with respect to two reference groups. Any suggestions for how to accomplish this would be most appreciated. Cheers, Alex -- 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/Support/Mailing_Lists/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/Support/Mailing_Lists