[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
ICTAS Doctoral Scholar
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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