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

rama david ramadavidgroup at gmail.com
Mon May 28 21:12:44 CEST 2012

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
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.???

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.

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.
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