> Bo wrote: > Thanks David. So to speak, as the center of mass of group SOL is not > free to move, we do not need stopcm to it. Another question is, does > it would be problematic in long time simulation without stopcm in such > situation, I mean the systematic errors caused by center of mass > motion. Thanks for clarification. > For a system with freeze group, we should not use any removal of com motions, and this system should still work. I don't find this relevant descriptions in gmx-manual, and it may be added into it. Yusong
> > > > tuyusong wrote: > > > 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: > > > > you can not only remove the com motion of one group. it is all (in one > > or more groups) or nothing. > > > > > > 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! > > > > End of gmx-users Digest, Vol 48, Issue 48 > > *************************************** > _______________________________________________ > 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
