[gmx-users] Re: Justin umbrella sampling tutorial......

Justin A. Lemkul jalemkul at vt.edu
Mon May 28 21:18:39 CEST 2012

On 5/28/12 3:12 PM, rama david wrote:
> Thank you Thomas and Justin for your valuable suggestion.
> Thomas and Justin, my Query is as follow......
> In step six ..We are doing NPT equilibration followed by production run....
> The mdp files for both is same(Except the time of run and saving of output)....
> So why the two mdp are same?????  Why we not restrain total protein for NPT
> equilibration (-DPOSRES)
> and then only POSRES_B (Position restrain on B chain, remove position restrain
> from other chain)
> for production run..(these we follow generally)???
> The main reason of confusion to me is the same mdp file in
> Equilibration(npt_umbrella.mdp )
> and production run (md_umbrella.mdp). So what is the difference between the NPT
> equilibration
> and production run.???

If one were to run an umbrella sampling simulation in each window without prior 
equilibration, you would normally discard the first few ns as equilibration. 
All the tutorial is telling you to do is to run some equilibration as a separate 
step.  You can approach the equilibration however you like.

> As per Thomas explanation I interpret the following Answer to my Queries..
> Please tell me  these are right or wrong ....
> */So if you want to calculate some equilibrium property of a protein in water you do
>   first a preperation simulation to equilibrate the system (NVE, NVT or NPT -
> depending
> for what ensemble you want the property).Normally during this you put position
> restraints
> to the protein backbone, so that the protein structure does not gets disturbed
> during the part where you equilibrate the water. but if your protein is fairly
> stable / rigid, you don't need these restraints./*
> So as the protein is stable thats why we are not using the position restrained
> in NPT..
> That is the reason the npt_umbrella.mdp and md_umbrella.mdp looks same.

More or less.  The special case with what you're doing in the tutorial is that 
you have no initiating velocities in each window; you only have coordinates. 
That's why it makes sense to do a bit of equilibration in each window first, 
generating velocities and re-equilibrating the system.


> Please accept my apology if I interpret any wrong and if unable to explain you
> my query..
> Thanks to Justin and Thomas for there valuable guidance....
> I will be a very greatfull to you if you help me to solve my simple  query..
> Thank you in advance...
> With Best Wishes,
> Rama David.


Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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