Oh, in fact I've posted a relevant topic earlier, but receive no reply. Here I want to do an AFM simulation using gromacs, pulling at the COM of a protein A, while keeping the COM of another protein B (which binds to A )fixed.
I do use pbc condition, and SPC water solvent sorrounding. I know I need simply add a restraint spring potential on the COM of B, but don't know how to implement it in detail. I notice that gromacs has a COM motion removal option and I might be able to remove the COM motion of B. But I think it does not actually do what I wanted, because I understand COM motion removal as simply substracting the velocity of whole system by the COM of B every nstcomm steps, it's like a transformation of coordinates which always set the COM of B as the origin, while the motion of the system actually remain the same as to no COM motion removal. So briefly, I just want to make sure 2 things: 1. how to fix the COM of a group 2. the algorithm in gromacs used to remove the COM motion thanks Below is the 4 previos mails in this topic, for convienence. I just don't know how to reply the mailing-list digest properly. ====================================================== zcwang wrote: > Yeah, maybe my discription is a little bit complicated. > > Well, what I understand of the center of mass removal, e.g. linear > removal, is that, the center of mass is not actually contrained or > restrained, it's just that all velocities in the system are simply > substracted by the velocities of the COM of the group every nstcomm > steps. > > So in fact, the COM of the group is still moving in absolute space, > right? The COM of the system is stationary unless you have periodic boundary condition (in which it fluctuates). The overall velocity is subtracted from all the atomic velocities. > > For example, if I add a force to a protein in a water enviroment while I > set the COM of the protein to be removed linearly, then the protein will > not actually stay stationarily in terms of COM as to the water > environment, but it will be dragged in the water environment, feeling > the friction of water mainly in the direction against the pulling > direction. > You probably wat to give the protein and the water opposite force such that the net force is zero. Or else I don't understand what you want to do... > I wonder if my understanding of the COM removal algorithm is right. > > > 在 2008-10-20一的 15:52 +0200，gmx-users-request at gromacs.org写道： >> zcwang wrote: >>> Hi all >>> I would like to know how gromacs remove center of mass motion? >> The COM velocity is the rate of change of the position of the COM, >> i.e. >> the mass-weighted average velocity of the particles. If you subtract >> that from each particle velocity, the COM velocity becomes zero. >> Likewise for angular motion, if applicable. >> >>> I thought it still allowed center of mass motion, but just did a >>> transformation of the coordinates at a certain frequency. >> I've never heard of GROMACS doing anything like that for this purpose. >> >>> It's just like looking at the system in a noninertial system >> attached to >>> the COM of the group. >>> Is that right? >> I don't know what you mean. >> >> Mark > > ________________________________________ _______________________________________________ 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
