RE: [gmx-users] AFM Pulling and com motion
From: "Zhou Bo" <[EMAIL PROTECTED]> Reply-To: Discussion list for GROMACS users To: Subject: RE: [gmx-users] AFM Pulling and com motion Date: Fri, 21 Sep 2007 00:49:21 +0800 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. MD is chaotic, so changing any detail will change the course of the simulation. Any ensemble averages should be the same, but for short runs, as the course example, you do not reach the ensemble average. I guess this is the reason for the difference. Berk. _ Live Search, for accurate results! http://www.live.nl ___ gmx-users mailing listgmx-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
RE: [gmx-users] AFM Pulling and com motion
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 >>To: >>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 listgmx-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 _ Talk with your online friends with Messenger http://www.join.msn.com/messenger/overview -- ___ 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 41, Issue 73 * ___ gmx-users mailing listgmx-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
RE: [gmx-users] AFM Pulling and com motion
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 To: 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 listgmx-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 _ Talk with your online friends with Messenger http://www.join.msn.com/messenger/overview ___ gmx-users mailing listgmx-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
RE: [gmx-users] AFM Pulling and com motion
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 listgmx-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
RE: [gmx-users] AFM Pulling and com motion
From: "Zhou Bo" <[EMAIL PROTECTED]> Reply-To: Discussion list for GROMACS users To: Subject: [gmx-users] AFM Pulling and com motion Date: Thu, 20 Sep 2007 11:06:09 +0800 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. _ FREE pop-up blocking with the new Windows Live Toolbar - get it now! http://toolbar.msn.click-url.com/go/onm00200415ave/direct/01/ ___ gmx-users mailing listgmx-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
