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)
Best,
Joerg
--
Joerg Sauter
Max Planck Institute of Colloids and Interfaces
Department of Theory & Bio-Systems
Am Mühlenberg 1
14476 Potsdam-Golm Germany
Fon: +49-(0)331-567-9622
--
gmx-users mailing list gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
* Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
