Thank you so much, Berk. I deeply appreciate of your comments. Jae H. Park
---- Original message ---- >Date: Tue, 11 Jul 2006 09:04:19 +0200 >From: "Berk Hess" <[EMAIL PROTECTED]> >Subject: Re: [gmx-users] Question about center-of-mass removal >To: gmx-users@gromacs.org > > > > >>From: Jae Hyun Park <[EMAIL PROTECTED]> >>Reply-To: Discussion list for GROMACS users <gmx- [EMAIL PROTECTED]> >>To: Discussion list for GROMACS users <gmx- [EMAIL PROTECTED]> >>Subject: Re: [gmx-users] Question about center-of-mass removal >>Date: Tue, 11 Jul 2006 00:27:55 -0500 >> >>Thank you, Mark. >> >>I have one more question for the confirmation. So, if there >>is other asymmetries (e.g. initially the fluid is at one >>side and the other side is empty, and as time goes on, it >>spreads to the empty side - non-equilibrium process. In flow >>direction there is no periodicty while periodic in other two >>directions), do I have to turn off the center-of-mass >>removal (e.g. nstcomm = 0) ? > >Everything depends on if your system has an absolute reference >in space, in Gromacs this can only be done with postion restraints >or freeze groups. >You have not written if this is the case. > >If there is no absolute reference, your com is uncoupled and you >should remove the com motion. >If you have an absolute reference you should not remove com motion >as this will influence the sampling in the system. > >Fluid flow itself has nothing to do with this. If the fluid flows in one >direction this is because of a force working on it and there should >be an equally large reaction force working on something else >in the opposite direction. > >Berk. > > >_______________________________________________ >gmx-users mailing list gmx-users@gromacs.org >http://www.gromacs.org/mailman/listinfo/gmx-users >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 ======================================= Jae Hyun Park, Ph.D. Postdoctoral Associate 3221 Beckamn Institute University of Illinois at Urbana-Champaign 405 North Mathews Avenue Urbana, IL 61801 (Tel) 217-244-4353, (FAX) 217-244-4333 (E-mail) [EMAIL PROTECTED] _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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
