Dear Amber users:
I am trying to compare a thermodynamic integration done with PME vs one
without PME, both in vacuum. But I am obtaining strange results. Maybe
somebody can point some error I am making inadvertently. So here is the
procedure I follow:
1) Build a system consisting only of a ligand, using xleap, and generate
from there the coordinate and parameter files. I'll use these two files to
run the ligand in vacuum, no PME, TI.
2) Take the coordinate file (restart format) in previous step and add a line
at the end of it, containing size and angles of the box.
3) Take the parameter file from step 1), and add three flags,
SOLVENT_POINTERS, ATOMS_PER_MOLECULE and BOX_DIMENSIONS.
4) Use files from 2) and 3) to run the ligand in vacuum with PME TI.
I imagine that there could be a problem in the addition of the flag
SOLVENT_POINTERS. My ligand has 68 atoms, so, since I want ligand in vacuum,
I use 1 1 69 for the arguments in that flag. Could this be an error? I use
69 because that number means where the solvent starts, and I don't want a
solvent.
The results that I get with these two calculations are -2.3 and +140, for no
PME and PME respectively. The difference seems too big to be due only to
Ewald; I would imagine the contribution of the ligand in the central cell
with the other ligands in the replicas to be relatively small, right?
Any idea?
Thanks,
Ignacio
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Received on Mon May 23 2011 - 13:30:02 PDT
