Even in the system with position-restrain, when only removing com of SOL group, gmx 3.3.3 also give the same error information as Bo:
Large VCM(group rest): 0.00001, -0.00002, -0.00000, T-cm: Inf Yusong -----Original Message----- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of David van der Spoel Sent: Thursday, April 17, 2008 3:21 AM To: Discussion list for GROMACS users Subject: Re: [gmx-users] Warning message with 3.3.3 but not with 3.3.1 Bo Zhou wrote: > Hi gmx-users, > > I want to simulate a solid/water interface. I just freeze the solid surface, > and let the water molecules free to move. Here is a part of my mdp as > follows: > > comm-mode = linear > nstcomm = 10 > comm-grps = SOL > > tcoupl = Berendsen > tc-grps = SOL Solid > tau-t = 0.1 0.1 > ref-t = 298 0 > > Same system and same sets were tested both in gmx 3.3.1 and gmx 3.3.3. > Following message in the log file was printed in the log file with gmx > 3.3.3, but not with gmx 3.3.1. > > Large VCM(group rest): 0.00001, -0.00002, -0.00000, T-cm: > inf > > Large VCM(group rest): 0.00001, -0.00003, -0.00000, T-cm: > inf > > Large VCM(group rest): -0.00000, -0.00003, -0.00000, T-cm: > inf > > I wonder whether it is reasonable to stopcm or not. Would it cause any > non-physical artifacts? Thanks for suggestions. stopcm tries to change the velocity of the rest group (solid) as well. Unfortunately you can not turn this off for one group. I'm not sure while this is different from 3.3.1, but since you have a solid reference you probably don't need to stopcm. > > _______________________________________________ > 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 -- David. ________________________________________________________________________ David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ _______________________________________________ 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 _______________________________________________ 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
