Hi Dechang Li, If your simulations are different, the results will be different. It's chaos!
Cheers, Tsjerk 2009/7/13 Dechang Li <li.d...@gmail.com>: > 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-us...@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 > -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623 _______________________________________________ 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