[gmx-users] Pull Code problems

Berk Hess gmx3 at hotmail.com
Tue Jan 13 16:55:11 CET 2009


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 100
> ps - that is OK I suggest. The problem is that pull group (pull_group1)
> 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 stays
> intact to track the movement of the group that is being pulled - pull
> group. Then how could this happen in my system? What should I do to pull
> only the pull_group1?
> 2/ I was recomended to use AFM pull mode in gromacs 3. What is the new
> name for AFM in gromacs 4? 
> Thanks.
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