[gmx-users] AFM Pulling and com motion

[Zhou Bo]

  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.