Filip Jagodzinski wrote: > hi gmx-users, > > i haven't been able to accomplish the following: > > i have a system with n atoms, and i want to remove the degrees of > freedom for some of the atoms during different moments of the simulation > > for example, assume the primary sequence of my protein is a-b-c-d-e-f-g, > and, for the first 50 picoseconds, i know that b, c and d move as a > "group", and so i want to remove the degrees of freedome between b and c > and between c and d, and have {bcd} move as one unit; then, at time > 50-100 picoseconds, atoms b, c and d no longer more as a group, but > atoms d, e, f and g move as a group, so for the integration step from 50 > to 100 picoseoncds, i would want to remove the degrees of freedome > between d and e, between e and f, and between f and g
I don't think this is possible within a single simulation. You would have to change your topology for each section of your simulations. You can add constraints to your topology or, if you want to keep the rigid parts of the protein a bit flexible, bonds of type 6. Depending on what you want to do, maybe it could also be sufficient to fit your simulation on some structure and always use the rigid part as fit group. cheers, jochen > > this is similar to fixing all but the active site of a protein and only > performing md on only the active site, but not quite the same > > any suggestions? > > thanks much! > > filip > > _______________________________________________ > gmx-users mailing list gmx-users@gromacs.org > http://www.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 [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > . > -- ************************************************ Dr. Jochen Hub Max Planck Institute for Biophysical Chemistry Computational biomolecular dynamics group Am Fassberg 11 D-37077 Goettingen, Germany Email: jhub[at]gwdg.de Tel.: +49 (0)551 201-2312 ************************************************ _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php