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
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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