[gmx-users] Re: Free energy calculation

[Fabian Casteblanco]

Thanks Justin.

Best regards,
Fabian

On Mon, Aug 8, 2011 at 5:49 PM, Fabian Casteblanco
<fabian.casteblanco at gmail.com> wrote:
> Hello all,
>
> I am setting up a free energy calculation (drug from full coulomb+vdW
> in solution --> drug with only vdW in solution --> dummy drug in
> solution).
>
> After reading most of the papers, I understand that you need
> significant overlap from the energies for each intermediate point to
> overlap so its best to have many intermediate points from Lambda=0 to
> Lambda=1.  The drug molecule I have is a bit complex but I wasn't sure
> if using too small of an intermediate could have a bad effect on the
> free_energy calculation.  I know Justin Lemkul said in its tutorial
> that Lambda=+0.05 should be good for most but I decided to go with
> Lambda=+0.02.  Could this have any negative effect other than taking a
> longer time?  Also, how does one come up with the best soft-core
> potential parameters to use?  Is it ok to use the one from the Methane
> in water tutorial?
>
> Thanks for everyone's expertise.
>
> --
> Best regards,
>
> Fabian F. Casteblanco
> Rutgers University --
> Chemical Engineering PhD Student
> C: +908 917 0723
> E:  fabian.casteblanco at gmail.com
>



-- 
Best regards,

Fabian F. Casteblanco
Rutgers University --
Chemical Engineering PhD Student
C: +908 917 0723
E:  fabian.casteblanco at gmail.com