Thank you very much again, David! Then it's fine for me, since what I want to do is a single point QM in "termalized" snapshots of the dynamics and not QM minimization.
Gustavo > [EMAIL PROTECTED] wrote: > > Dear GROMACS Users, > > > > I'm trying to use GROMACS to get some MD snapshots for single-point > quantum > > mechanical calculations, trying to observe HOMO-LUMO gap of a protein > immersed > > in water with counterions, at a given salt concentration (4600 atoms in > total). > > I'd like to know if they are reliable enough to send to QM calculations. > I've > > got two questions: Which are the criteria I should be looking at? And one > of > > them I've analyzed was energy conservation (I'm doing 300K NVT MD, with 10A > > cutoff for vdw and coulomb, with PME electrostatics, and double precision), > and > > the manual says a Ekin RMSD/Tot Energy RMSD ratio below 0.05 is fine, but > I've > > got 0.3-0.5 in all simulations I've done. What should I do? > > > This is because of T coupling. If you turn off T coupling it will be > better (but you will not have constant T, and the energy will dirft in > the long run). Your starting structures are fine for QM, but QM > minimization will take a LONG time. > > > > Thanks in advance, > > > > Gustavo Troiano Feliciano > > > > > > ---------------------------------------------------------------- > > This message was sent using IFUSP Webmail - USP/Sao Paulo/Brazil. > > _______________________________________________ > > gmx-users mailing list [email protected] > > 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 > > > -- > David van der Spoel, Ph.D. > Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University. > Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755. > [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se > _______________________________________________ > gmx-users mailing list [email protected] > 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 > ---------------------------------------------------------------- This message was sent using IFUSP Webmail - USP/Sao Paulo/Brazil. _______________________________________________ gmx-users mailing list [email protected] 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
