[gmx-users] Reg:Equilibration

[Mark Abraham]

----- Original Message -----
From: Anil Mhashal <anil2000.2008 at gmail.com>
Date: Tuesday, October 5, 2010 23:11
Subject: Re: [gmx-users] Reg:Equilibration
To: Discussion list for GROMACS users <gmx-users at gromacs.org>

> Just plot a graph of the potential energy with respect to the time and check the energy fluctuation, it should be less than 10% of the average potential energy then u can say that ur protein is equilibrated.

Well, you can suppose that the potential energy is approximately equilibrated, but that might not relate to the equilibration of the properties of interest. Different observables relax on different time scales.

Mark

> On 5 October 2010 17:16, vinothkumar mohanakrishnan <kmvinoth at gmail.com> wrote:
>  hi anil
> 
> i get the potential energy at the end of the mdrun. if i want to calulate the deviation with what i should compare and calculate the deviation.can you be more specific.
> 
> Regards
> Vinoth > 
> 
>  On Tue, Oct 5, 2010 at 4:51 PM, Anil Mhashal <anil2000.2008 at gmail.com> wrote:
>    To check ur equilibration, just look at the potential energy and find out the deviation in the energy if the deviation in the energy is within 10% then ur equilibration is successful... 
> 
  > On 5 October 2010 14:56, vinothkumar mohanakrishnan <kmvinoth at gmail.com> wrote:
 > Hi all
> 
> Suppose say i have a box of decane molecules and i want to equilibrate. say i have all the necessary files to run mdrun. on what basis i say whether my equilibration is successful r not after the mdrun. what properties i should measure to know whether my equilibration was successful.
    > 
> Regards
> Vinoth
 > 
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>   Anil R.Mhashal
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> National Chemical Laboratory> Pune > 
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> Anil R.Mhashal
> Research fellow Physical Chemistry Division
> National Chemical Laboratory> Pune > 
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