On 08/05/2013 01:54 PM, Justin Lemkul wrote:
On 8/5/13 7:44 AM, Joerg Sauter wrote:
Dear all,
I am trying to compute the free energy of hydration for cellobiose (a
beta (1-4)
glucose dimer) using BAR in Gromacs 4.6.1. However, I encounter a
problem.
I find that the vacuum conformations of the molecule in a regular vacuum
simulation differ from the conformations in the decoupled simulation
in the free
energy case i.e., with the additional mdp entries:
free-energy = yes
init-lambda = 0
couple-lambda0 = none
couple-moltype = solute
couple-intramol = no
Here is a histogram of the dihedral angles of the glycosidic linkage in
the vacuum case
https://dl.dropboxusercontent.com/u/70358077/reg.pdf (it stays in the
global
free energy minimum)
and this is the decoupled free energy case (same starting
conformation in the
global free energy minimum)
https://dl.dropboxusercontent.com/u/70358077/fe.pdf
I understand that Gromacs replaces the intramolecular interactions
with explicit
pair
interactions. Therefore, I had to increase table-extension but that
did not
change much. I was thinking that maybe this could be a problem
specific to this
topology (a GLYCAM06h conversion from Amber), however, I do not see
how this can
occur.
I hope someone has an idea what is going wrong.
mdp file: https://dl.dropboxusercontent.com/u/70358077/md.mdp
(same behaviour
for longer runs)
top file: https://dl.dropboxusercontent.com/u/70358077/cellob.top
gro file: https://dl.dropboxusercontent.com/u/70358077/cellob.gro
This is sort of a minimal example. The same problem occurs
in a regular simulation when decoupling from water using multiple
lambdas.
Have you tried running with rlist=rcoulomb=rvdw = 0 rather than 99?
If nothing else, I would try again with version 4.6.3. There have
been tons of fixes to the free energy code since 4.6.1, though I don't
know offhand which, if any, would be affecting your results.
Regardless, the current version should always be the "best" version ;)
-Justin
Hi Justin,
I just tried it with version 4.6.3. and rlist=rcoulomb=rvdw = 0.
Unfortunately, I get the same results.
Best,
Joerg
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