[gmx-users] PMF using umbrella sampling

[Berk Hess]

> Date: Tue, 1 Sep 2009 09:45:35 -0500
> Subject: Re: [gmx-users] PMF using umbrella sampling
> From: bobjohnson1981 at gmail.com
> To: gmx-users at gromacs.org
> 
> Can you use runtype=constraint in parallel? I switched to using
> runtype=umbrella because I received error messages that the
> constraints can't be run in parallel.

With 3.3 you can not (or you actually could if you have both
groups on cpu 0 and remove the error).
With 4.0.5 the complete pull code works properly in parallel.

Berk

> 
> Also...yes...I switched up angstroms and nanometers...I don't know how
> many times I've made that mistake and couldn't find it myself...
> 
> Thanks,
> Bob
> 
> On Tue, Sep 1, 2009 at 2:34 AM, Berk Hess<gmx3 at hotmail.com> wrote:
> > Hi,
> >
> > Firstly, you are not constraining (runtype=constraint), but using a harmonic
> > umbrella potential.
> >
> > Secondly, your distance of 28.9 nm seems enormous, maybe you mixed
> > up nanometers and Angstroms here?
> >
> > Thirdly, I would strongly suggest to switch to Gromacs 4.0.5.
> > I have completely rewritten the pull code for Gromacs 4
> > and things now work much easier and better.
> >
> > Berk
> >
> >> Date: Mon, 31 Aug 2009 12:18:06 -0500
> >> From: bobjohnson1981 at gmail.com
> >> To: gmx-users at gromacs.org
> >> Subject: [gmx-users] PMF using umbrella sampling
> >>
> >> Hello everyone,
> >> I'm trying to compute the PMF for pulling two proteins apart. I'm
> >> planning on setting up several runs where the COM separation of the
> >> proteins is constrained and the constraint force is measured over the
> >> course of a long simulation. However, I'm having trouble doing this
> >> because I'm unsure of the inputs in the .ppa file. I'm trying to do
> >> this with Gromacs 3.3.3. Here is the .ppa file I'm using:
> >>
> >> runtype = umbrella
> >> ngroups = 1
> >> reference_group = knob
> >> reftype = com
> >> pulldim = Y Y Y
> >> group_1 = car
> >> k1 = 1000
> >> pos1 = 0.0 0.0 28.8989219666
> >>
> >> Here, there are two proteins: car and knob. The COM of car is located
> >> at (0.0 0.0 28.8989219666) relative to knob. The problem I'm
> >> experiencing is that the simulation results in the two proteins being
> >> pulled apart instead of constrained at distance pos1. I believe that
> >> I'm misinterpreting the inputs. Does anyone know the solution?
> >> Thanks,
> >> Bob
> >> _______________________________________________
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> >
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> 
> 
> 
> -- 
> Bob Johnson, PhD
> Institute for Computational Molecular Science
> Temple University
> 1900 North 12th Street
> Philadelphia, PA 19122
> http://www.sas.upenn.edu/~robertjo
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