[gmx-users] Re: Free Energy Calculation

[David Mobley]

Hi,

Sorry for the delay answering. These questions are better put on the  
GROMACS users list.

1) Yes -- the Berendsen barostat does not sample the correct  
distribution of pressures.
2) Regenerating velocities is fine for a couple of reasons: (a) we are  
after thermodynamics, not dynamics, and (b) regenerating velocities  
does not de-equilibrate the system (see the Andersen thermostat, for  
example).



On Jun 8, 2009, at 3:02 PM, Mauricio Carrillo Tripp wrote:

> Hi,
>
> I've been following directions at http://www.dillgroup.ucsf.edu/group/wiki/index.php/Free_Energy:_Tutorial
> to calculate hydration free energies of a few small molecules, and I  
> have a couple of questions:
> 1) Is there a reason for using NVT instead of NPT for the production  
> step?
> 2) I noticed that between the equilibration and the production runs  
> you generate velocities at each step,
>     instead of using the ones from the previous step. Is there a  
> reason for doing this? wouldn't this
>     'de-equilibrate' an already equilibrated system?
>
> Thank you.
>
> -- 
>         0     |  Mauricio Carrillo Tripp, PhD
>      /         |     Department of Molecular Biology, TPC6
>  0            |     The Scripps Research Institute
>      \         |     10550 North Torrey Pines Road
>         0     |     La Jolla, California 92037
>      /         |     trippm at scripps.edu
>  0            |  http://www.scripps.edu/~trippm
>
> ** Aut tace aut loquere meliora silentio **

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