David wrote: > you can not only remove the com motion of one group. it is all (in one > or more groups) or nothing.
Thank you for replying. Do you mean, that it must be nothing when system has any freeze groups? Yusong. -----Original Message----- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of David van der Spoel Sent: Thursday, April 17, 2008 4:01 AM To: Discussion list for GROMACS users Subject: Re: [gmx-users] Warning message with 3.3.3 but not with 3.3.1 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! 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
