RE: [gmx-users] AFM Pulling and com motion

From: Zhou Bo [EMAIL PROTECTED] Reply-To: Discussion list for GROMACS users gmx-users@gromacs.org To: gmx-users@gromacs.org 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

RE: [gmx-users] AFM Pulling and com motion

From: Zhou Bo [EMAIL PROTECTED] Reply-To: Discussion list for GROMACS users gmx-users@gromacs.org To: gmx-users@gromacs.org 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

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

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 gmx-users@gromacs.org To: gmx-users@gromacs.org Subject: RE: [gmx-users] AFM

RE: [gmx-users] AFM Pulling and com motion

for GROMACS users gmx-users@gromacs.org To: gmx-users@gromacs.org 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

[gmx-users] AFM Pulling and com motion

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