Thanks for your reply. There is no absolute reference here. The system is just from this web site "http://www.csc.fi/english/research/sciences/chemistry/courses/gmx2007"; (hands-on: The pull package). I really do not know the advantage or necessity of stopcm in SMD, because when I test the two systems, with and without stopcm, there is a distinct difference between the calculated pull force.
>You didn't tell if you are using an absolute reference or not. >With an absolute reference you should not remove the com motion. >Berk. >>From: "Zhou Bo" <[EMAIL PROTECTED]> >>Reply-To: Discussion list for GROMACS users <[email protected]> >>To: <[email protected]> >>Subject: RE: [gmx-users] AFM Pulling and com motion >>Date: Thu, 20 Sep 2007 22:44:29 +0800 >> >> Thanks to Berk. I just tested two system, one with stopcm and the other >>without stopcm. I calculated the pull forces and compared them with each >>other. There are really some distinct differences between them during the >>80ps simulation. I worry about it, for example, in long time simulations, >>so I want to know which one is the better and reliable choice, stopcm or >>without stopcm. As I know, the NAMD package only removes the initial center >>of mass motion. >>Thanks for your reply. >> > >>Hi GXM Users, > >> I'm trying to execute some AFM Pulling. I followed the pull code >tutorial > >>from GMX WORKSHOP 2007, and I found there is no specific to com motion >in > >>mdp, so the default is "comm-mode=Linear" and "comm-grps=System". I was > >>confused about it as I believed we should not stopcm when doing AFM >Pulling > >>because of the external force. Does it problematic to stopcm when doing >AFM > >>Pulling? > >> > >>Thanks! > >> > > >This depends on what type of pulling you are doing. > >If you have an absolute reference you are right. > > >But when you pull between two groups of atoms, there are no > >external forces, but internal forces between two groups. > > >Berk. > >_______________________________________________ >gmx-users mailing list [email protected] >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 _________________________________________________________________ Talk with your online friends with Messenger http://www.join.msn.com/messenger/overview ------------------------------ _______________________________________________ gmx-users mailing list [email protected] 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 41, Issue 73 ***************************************** _______________________________________________ gmx-users mailing list [email protected] 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
