[gmx-users] Re: Pull code

Thomas Schlesier schlesi at uni-mainz.de
Thu Jul 1 16:57:07 CEST 2010

The force acting on your pulled group is:
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.


> 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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