Reza Salari wrote:
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).
That looks like a perfect excuse to learn how to write a shell or other
script. Off the top of my head, I think all you need is a loop over the
range of protein atom numbers written to a file that you can #include in
your main topology.
Here are my questions:
1) Isn't there any other solution for this problem?
Not that I know of.
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?
True, the mesh contribution of a frozen group should be constant if the
box stays the same size (OK, it is PME, approximately constant), and
will be approximately constant if the box does vary a little. Thus the
error introduced in comparing total energies is small. Since there are
no forces on the protein atoms, I think that the mesh contribution to
forces will have no appreciable effect, thus the dynamics would be OK.
However, the [exclusions] solution is so simple it seems poor economy
not to use it.
Mark
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