[gmx-users] Re: Pull code

Gavin Melaugh gmelaugh01 at qub.ac.uk
Thu Jul 1 17:56:51 CEST 2010

Hi Thomas

Thanks for your help



Thomas Schlesier wrote:
> The force acting on your pulled group is:
> F=k(vt-x)
> where x is the displacment of that group (1) relativ to group (0).
> I thin Justin used this values to create the structure for the later
> umbrella sampling, so the pulling velocity is rather fast.
> I usually used k1=500, and velocities of about 0.001 to 0.0001 for
> pulling experiment for systems with only a few hydrogen bonds.
> I think the choice of the parameters depends upon how strong your
> molecules interact with another.
> But for umbrella sampling i would assume that it matters most that you
> generate strucutres with the right distance and not so much with what
> pulling velocity you reached this distances.
> Greetings
> Thomas
>> Hi Justin
>> Thanks for your help. The two molecules are now moving together. I am
>> however slightly confused about the parameters pull_rate1 and pull_k1. I
>> want the molecules to come together very slowly therefore
>> I would set the rate to be a very small value. How the does the force
>> come into play and how should you decide on the best value?
>> Gavin
>> Justin A. Lemkul wrote:
>>> Gavin Melaugh wrote:
>>>> Hi Justin
>>>> Thanks. If I use the pull_geometry = direction I would go for the
>>>> following jus t to pull the molecules together in the z direction.
>>>> pull        = umbrella
>>>> pull_geometry = direction
>>>> pull_start = yes
>>>> pull_ngroups = 1
>>>> pull_group0 = cage_1
>>>> pull_group1 = cage_2
>>>> pull_vec1 = 0.0 0.0 -1.0
>>>> pull_rate1 = 0.01
>>>> pull_k1 = 1000
>>>> Does this seem reasonable? Also in the pull_rate what is meant by the
>>> Probably.  Try it.
>>>> 'rate of change of the reference position'? (Is it the position of the
>>>> reference group, if so what if I don't want it to change?)
>>> It is the rate of change of the reference position, which is the
>>> position at the outset of the simulation.  Your objective is to pull
>>> your two species together, right?  I don't see why you wouldn't want
>>> it to change.  You're not changing anything about pull_group0 (your
>>> reference group), since you aren't setting pull_rate0.  Everything is
>>> applied to pull_group1 (hence _rate1, _k1, etc).
>>> -Justin
>>>> Cheers
>>>> Gavin

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