# [gmx-users] Pull Code problems

Berk Hess gmx3 at hotmail.com
Tue Jan 13 18:25:26 CET 2009

```Hi,

If you pull without a reference, you will be doing nothing in the limit
of slow pulling. For fast pulling you will be doing something.

pull_start=yes
pull_init1=0
will initialize set pull_init to the initial distance.

Berk

> Subject: RE: [gmx-users] Pull Code problems
> From: genesup at gmail.com
> To: gmx-users at gromacs.org
> Date: Tue, 13 Jan 2009 19:59:38 +0300
>
> OK,
>
> 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?
> SDA
>
> P.S.
> In my understanding to do that I should leave reference group blank and
> specify pull group only:
> ﻿pull_group0=
> ﻿pull_group1=r_535
> 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:
> > Hi,
> >
> > 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).
> >
> > Berk
> >
> > > 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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