[gmx-users] Free energy calculation

Fabian Casteblanco fabian.casteblanco at gmail.com
Mon Aug 8 23:49:17 CEST 2011

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

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

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