[gmx-users] thermodynamic integration yields different values in gromacs 3.3.1 and later versions

Schneck at uni-heidelberg.de Schneck at uni-heidelberg.de
Tue Jun 8 14:01:00 CEST 2010

Dear Gromacs users,

I am doing thermodynamic integration in order to compute the change in free
energy upon increasing the electric charges of a water molecule from zero
(lambda=0) to its actual partial charges (lambda=1). I get significantly
different results of <dVpot/dlambda> with Gromacs 3.3.1 on one hand and 3.3.3
(and later versions) on the other hand. I use linear scaling of the charges
with lambda.

There is a difference for all lambda values but it's most prominent near
lambda=0, where the values are different by an order of magnitude. The
difference is independent of the trajectory, i.e., when I use the trajectory
generated with 3.3.1 and rerun it with 3.3.3, I get the same results as if I
had generated the trajectory with 3.3.3 directly.

Is this a known phenomenon?
Can anyone tell me what is the difference between versions 3.3.1 and later
versions in this context?
Are there any "hidden" corrections that have been added between 3.3.1  
and 3.3.3?



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