[gmx-users] Pull Code problems
genesup at gmail.com
Tue Jan 13 17:59:38 CET 2009
finally I try to simplify my question by revealing my final aim.
I have a group that I want to pull out of my protein. I want only one
group to be pulled out in one direction.
How could I do that?
In my understanding to do that I should leave reference group blank and
specify pull group only:
In this case grompp calculates initial distance from (0,0,0) to pull
group and sets the initial force to a very high value
(distance*force_constant) instead of 0. To correct this and to make the
initial pull rate = 0 I should set pull group to the center of
coordinates or set the initial position of the pull spring to the
position of the pull group. How should I do that?
On Tue, 2009-01-13 at 16:55 +0100, Berk Hess wrote:
> The pull option acts between COM's. Both COM's will move.
> If not, you would have a net force on the COM of the whole system.
> The AFM option is no longer there.
> I never understood what the difference between Umbrella and AFM was.
> But Umbrella (as well as constraint) should be able to do all things
> that were possible before (and more).
> > Subject: Re: [gmx-users] Pull Code problems
> > From: genesup at gmail.com
> > To: gmx-users at gromacs.org
> > Date: Tue, 13 Jan 2009 18:44:36 +0300
> > OK,
> > I have a new problem.
> > I`ve started the simulation with the following pull parameters
> > ;-----------PULL CODE ---------------------
> > pull<-->=<-----> umbrella
> > pull_geometry<->= direction
> > pull_group0<-->= r_500
> > pull_group1<--->= r_535
> > pull_vec1<----->= -1.306 1.355 -0.319
> > pull_k1><------>= 1000
> > pull_rate1<---->= 1 ; nm/ps = 1 A/ns
> > With such extreme pulling velocities I had my system teared apart in
> > ps - that is OK I suggest. The problem is that pull group
> > and reference group (pull_group0) were both pulled in opposite
> > directions - pull_vec1 and -(pull_vec1)?!
> > 1/ In my best understanding the reference group is the one that
> > intact to track the movement of the group that is being pulled -
> > group. Then how could this happen in my system? What should I do to
> > only the pull_group1?
> > 2/ I was recomended to use AFM pull mode in gromacs 3. What is the
> > name for AFM in gromacs 4?
> > Thanks.
> > _______________________________________________
> > gmx-users mailing list gmx-users at gromacs.org
> > http://www.gromacs.org/mailman/listinfo/gmx-users
> > Please search the archive at http://www.gromacs.org/search before
> > Please don't post (un)subscribe requests to the list. Use the
> > www interface or send it to gmx-users-request at gromacs.org.
> > Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> Express yourself instantly with MSN Messenger! MSN Messenger
More information about the gromacs.org_gmx-users