[gmx-users] Large dV/dlambda value at lambda = 0

Robert Johnson bobjohnson1981 at gmail.com
Mon Dec 22 18:22:27 CET 2008

Hello everyone,
I'm computing the relative binding free energies of DNA bases on a
nanotube using the protocol listed here:
I'm using the following steps:
1. Turn off all charges on base
2. Transform LJ parameters
3. Turn on all charges

Because the transformation (from G to A for example) involves changing
every single atom charge, I decided to first reduce all charges to
zero. The problem I'm experiencing occurs at small lambda values
during step 2 (transforming LJ parameters) of the above routine. I
obtain large dV/dlambda values of about 2E3 for lambda 0.05 or less.
The rest of the curve contains dV/dlambda of about 6E2. I don't think
this is due to any equilibration issues. Each lambda point is run for
15 ns and I incur a small error of ~1E-1 for each dV/dl value. The
error is a little bit larger (~1) for the lambda=0 point. I believe
the topology and simulation protocol is correct. I have already run
calculations for the absolute binding free energy of this system and I
get good agreement for steps 1 and 3. However, it seems that step 2 is
problematic. If I can't get rid of the large dV/dlambda value, how
should I handle that? Is this large value an artifact? Or should I
assume that the "real" dV/dl curve can be extrapolated to a value that
is more reasonable and in better agreement with the rest of the curve?
If anyone has some suggestions on how to alleviate this problem, I'd
appreciate reading them.


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