[gmx-users] Re: Umbrella Sampling - Justin tutorial

Steven Neumann s.neumann08 at gmail.com
Thu Nov 17 14:48:04 CET 2011

Thank you Justin, I will read it for sure and come back to my simulations!


On Thu, Nov 17, 2011 at 1:25 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:

> Steven Neumann wrote:
>> Hi Justin,
>>  I am sorry for so many questions but I do not understand something.
>> First we run the simulation of pulling Chain A from ChainB with constant
>> force (pull_k1=1000) and constant velocity of pulling (pull_rate1=0.01) We
>> extract windows as we discussed and then run simulations with those
>> configurations as a starting point. I saw the trajectory of one of these
>> simulations and it looks like normal MD simulation. My question is: Why do
>> we have in mdp file still pull code as we do not pull protein chain any
>> more? Pull rate is set to zero but force is still applied... why? Is this
>> code just used to extract pullf.xvg and pullx.xvg which does not change too
>> much?
>> I would appreciate the explanation as without undesratnding the basics
>> its not good to do any simulation like this.
> Have you read the WHAM paper, or the one specific for g_wham, or perhaps
> papers about umbrella sampling in general?  You should start there before
> diving in to doing the simulations.
> The harmonic force applied in the SMD and US simulations is simply a
> biasing force to make something happen.  With a non-zero pull_rate, motion
> in a particular direction is forced to happen.  With a pull_rate of zero,
> the COM distance is simply restricted - the biasing force maintains the COM
> distance between the two defined species, while allowing it to oscillate
> according to a harmonic force defined by pull_k1.  Thus you establish
> sampling overlap between neighboring windows along the reaction coordinate.
> -Justin
> --
> ==============================**==========
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
> ==============================**==========
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