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

Justin A. Lemkul jalemkul at vt.edu
Thu Nov 17 14:25:46 CET 2011

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 A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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