[gmx-users] Free_energy size selection

Fabian Casteblanco fabian.casteblanco at gmail.com
Tue Aug 16 17:33:06 CEST 2011

Hello all,

I'm running a free energy simulation using BAR method for a one drug
molecule in several alcohols.  I started off using 500 solvent
molecules for but realized it was taking too long for the smaller
solvents, which would make the larger solvents even more time
consuming.  I reduced it to two test cases. One using 210 solvent
molecules and another using 300 solvent molecules.  From what I've
read on the user archives,  the pressure will always oscillate and for
smaller systems, the oscillations will be even larger.  For example,
on my 210 solvent case, after 1000 ps, the pressure is 1.7 bar
(reference set to 1 bar).  Is this due to the pressure oscillations?
Will running for even longer times eventually make the error at least
a bit smaller?  Is this ok for free energy calculations?

Thanks for your expertise.  Your help is appreciated.

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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