[gmx-users] PMF using umbrella sampling

Berk Hess gmx3 at hotmail.com
Tue Sep 1 09:34:23 CEST 2009


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.


> 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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