Dear all, I have did a simulation with explict water model using Gromacs-3.3.3. To save the hard disk space, I didn't collect the coordinates of water by using the following parameters:
dt = 0.002 ; ps ! nsteps = 30000000 ; total time. nstcomm = 1 nstxout = 30000000 ; nstenergy = 1000 nstvout = 30000000 nstlog = 20000 nstxtcout = 1000 xtc_grps = Protein In addition, I did a short simulation of the system in which the coordinates of water were collected every 2 ps. For comparison, I calculated the RMSD of C-alpha atoms of the protein. However, the values are different of the two systems! Are these differences reasonable? BTW: I didn't generate the velocities in the beginning. RMSD of C-alpha atoms without collecting water coordinates: @ subtitle "C-alpha after lsq fit to C-alpha" 0.0000000 0.0001220 2.0000000 0.0545500 4.0000000 0.0691709 6.0000005 0.0657938 8.0000000 0.0723884 10.0000000 0.0800556 12.0000010 0.0745629 14.0000010 0.0732903 16.0000000 0.0752474 18.0000000 0.0774800 20.0000000 0.0914096 22.0000019 0.0981914 24.0000019 0.0983810 26.0000019 0.1057151 28.0000019 0.1053288 30.0000019 0.1084988 RMSD of C-alpha atoms with collecting water coordinates: @ subtitle "C-alpha after lsq fit to C-alpha" 0.0000000 0.0002658 2.0000000 0.0569104 4.0000000 0.0642647 6.0000005 0.0673439 8.0000000 0.0760661 10.0000000 0.0837568 12.0000010 0.0978260 14.0000010 0.1037093 16.0000000 0.1087546 18.0000000 0.1126641 20.0000000 0.1321630 22.0000019 0.1270466 24.0000019 0.1102782 26.0000019 0.1115073 28.0000019 0.1304575 30.0000019 0.1173159 Best regards, ========================================= Dechang Li, Ph.D Candidate Department of Engineering Mechanics Tsinghua University Beijing 100084 P.R. China Tel: +86-10-62773574(O) Email: lidc02 at mails.tsinghua.edu.cn ========================================= _______________________________________________ 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