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?
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
