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

[rama david]

> 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.???
>
> 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.....(Thomas Explanation)
> *
> my Interpretation is as follow ....
>


> 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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