[email protected] wrote:
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?
Are you using PME? There is a bug in the 3.3.1 free energy code with PME. It
is a known issue, but unfortunately it looks like the mailing list search is
down so I can't locate the thread where this is discussed.
-Justin
Thanks
Emanuel
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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