On 8/5/13 9:52 AM, Joerg Sauter wrote:
On 08/05/2013 02:15 PM, Justin Lemkul wrote:
On 8/5/13 8:12 AM, Joerg Sauter wrote:
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.
OK, good to know. We can rule out 4.6.1-era bugs, then. Does visualization
or an analysis of energy terms stored in the .edr file provide any clues as to
the source of the problem?
-Justin
Visualization does not show any abnormalities beyond odd confomations in the
free energy coupling case.
Regarding the energies: I am not sure whether this is normal behaviour, but, in
the free energy coupling case I do not see energy values for LJ 14 or Coulomb 14
interactions. I thought that by selecting couple-intramol=0 all intramolecular
interactions would be replaced by pairtype (14) interactions.
In addition, for Coulomb (SR) I get in the free energy case
LJ (SR) -22.8084 0.076 5.90879 -0.379238 (kJ/mol)
in comparisson to
LJ (SR) 16.8295 0.81 13.2303 4.51371 (kJ/mol)
in the regular vacuum simulation. So this looks like the 14 interactions get
shifted to the LJ/Coulomb terms in the coupling simulation?! (However, the
numbers do not add up)
This is smelling buggy to me, and there have been issues with 1-4 interactions
in the free energy code before (http://redmine.gromacs.org/issues/1225), so
there could be a lingering problem. Hopefully Michael will chime in. It might
be worthwhile to open up a bug report on redmine.gromacs.org with all of the
information you have provided (input files, output data, and the very nice
description of the issue you have posted).
-Justin
--
==================================================
Justin A. Lemkul, Ph.D.
Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalem...@outerbanks.umaryland.edu | (410) 706-7441
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