Hi Warren, if you want to use distance restraints, the two proteins must be in the same gromacs "molecule". AFAIK, it is impossible to use distance restraints between atoms of different molecules. Altermatively, you may want to consider bonds of type 6 (not subject to lincs).
pdb2gmx -merge is useful to create the topology of a "molecule" that actually contains 2 proteins. If the two proteins must be in different gromacs "molecules", you would have to use the pull code. Best, Jochen warren deng wrote: > Hi Gromacs users, > > In my simulation, I need to restrain distances between atoms on two protein > molecules. But the Gromacs manual on NOE seems to imply that the atom > indices belong to the same molecule type. > > So I am wondering whether it is possible to create distance restraint > between two molecule types in Gromacs? > > Many thanks, > > Warren > > > > ------------------------------------------------------------------------ > > _______________________________________________ > 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 gmx-users-requ...@gromacs.org. > 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php