Hi, > > if i just use the topology of the sugar without the protein then the > simulations starts but the atoms are not moving during the simulation. they > are exactly at the same position in frame 1 and frame n. therefore had the > idea to use the build-in x2top function. so i would be glad to get it > somehow working... >
Well, I don't see how a topology from x2top would do different than one from PRODRG or one generated properly. PRODRG doesn't write position restraints. Did you happen to have integrator set to steep in the .mdp file? I get the impression that you first have to come to terms with Gromacs and performing simulations, before trying to do the combination protein/sugar. But that may just be me. Tsjerk -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623 _______________________________________________ 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
