Hi! Is this with GBSA implicit solvent, and in that case what Born radii model? Could you mail me the tpr off-list, and I'll have a look at it.
Cheers /Per 5 aug 2010 kl. 20.26 skrev Elio Cino: > > Since the charmm force field has some instances with large charge groups > (grompp warns you for it) it is advisable to use a longer cut-off (or no > cut-off at all, by setting them all to 0). I've run 200 ns simulations with > 1.5 nm and nstlist = 5 and a timestep of 2 fs and constraints = all-bonds. > I could not have them set to infinite because I am using PBC. I used 1.5 and > the system ran fine with 2fs timestep. On another note, I installed 4.5 beta2 > on another computer today and using the exact same system and settings I get > tons of lincs errors (bond rotate over 30 deg) and cannot even do position > restrain dynamics without segmentation fault. I even tried using the exact > same tpr files as my successful runs. The one that works was my laptop (OSX > 10.6 core2 duo) and the one that fails is centos5 dual quad core xenon. If I > run a normal solvated simulation, the linux machine runs fine. > > Elio Cino > -- > 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
