Dear all, I used Gromacs-3.3.1 to simulate a small protein in water. I have used 2 and 16 CPUs to do the simulation respectively. But I got the RMSD of the protein equilibrated to 0.15 nm in the 2 CPUs simulation and 0.20 nm in the 16 CPUs one. Are these differences reasonable? In the 16 CPUs simulation, the RMSD of protein at t=0 was about 0.1 nm, why not equal to zero? I used the initial structure for the least squares fit.
Best regards, 2008-4-5 ========================================= Dechang Li, PhD Candidate Department of Engineering Mechanics Tsinghua University Beijing 100084 PR China Tel: +86-10-62773779(O) Email: [EMAIL PROTECTED] ========================================= _______________________________________________ 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
