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.
Thank you,
Joerg
--
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
