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 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