Hi everybody,
I want to do a simulation using frozen groups and it seems it is much more
difficult than I first thought. I searched the mailing list and I still have
problems that I can't figure out. It is much appreciated if help me with these
problems or point me in the right direction.
The scenario is this: I have a protein and a ligand and I want to do free
energy calculation. I want to freeze the protein (for a couple of reasons but
mainly because it is a big protein and I want to save computation time so I
don't want to use restraints) and I know these about freezing the protein
(please correct me if any of them is incorrect):
-- For minimization, it seems only steep algorithm works.
-- I should not use pressure coupling and any constraints (bonds,...) for
frozen groups.
-- In my mdp file for production run, I defined these:
coulombtype=pme
energygrps=protein ligand SOL
energygrp_excl=protein protein
freezegrps=protein
freezedim= Y Y Y
comm_mode=no
-- I know that I should use GROMACS 4.0.2 with fixed freeze code.
Now when I want to run the grompp for production mdp, I get this warning:
" can not exclude the lattice coulomb energy between energy groups"
I know that this is because I used pme and it seems that I have only two
options to solve it: either use other types of long range electrostatics that
don't use lattice sum (which I don't want to, because I think PME is much
better than others; also I have important electrostatic interactions at
protein-ligand interface so I want to use the best method for electrostatics)
or use [ exclusions ] part of topology file to exclude interactions of every
pair of atoms in the protein (I saw this solution in the mailing this, which is
really cumbersome in my case because the protein is big, but I'll do that if I
have to).
Here are my questions:
1) Isn't there any other solution for this problem?
2) Is that warning really critical? I mean if I am going to compare the two
states of the same protein (same protein with different ligands), don't those
"unexcluded coulomb energies" cancel out each other when comparing the total
energies of the two states? Or there is no guarantee for this?
Thank you in advance. Any kind of help is really appreciated.
Reza Salari
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