Hello RISM experts,
I am running 3DRISM calculations on snaps taken from an MD run, to try and
estimate solvation energy. The snaps were slightly altered after the MD
(extra proton, appropriate change to .top file, followed by minimise in
Generalised Born with heavy atoms restrained).
I'm using an .xvv for SPC water with 1M of Cl- ions present. The peptide
has net positive charge.
GB energy is well-behaved, but I get wildly different RISM energies (100s
kcal/mol) for different groups of very similar-looking snaps, this is
traceable to specific terms in the output:
--solvent PE
--Partial Molar Volume
--dcf Integral
Kirkwood-Buff is not affected, it is fairly smooth.
What could cause such big changes in the PMV terms? I don't see anything
special by plotting out the volumetric info although I am not an expert.
I'm cautious about just going ahead and do a RISM minimise because the
outliers are *down* in energy from the main bulk of the snaps (and its
expensive, of course).
Josh
**********************************************
Input file is pretty standard afaik:
&cntrl
ntx=1, ntpr=1, ntwx=1,
imin=5, maxcyc=1, !Single-point energy calculation
ntb=0, !Non-periodic
cut=9999., !solute-solute interactions
irism=1,
/
&rism
tolerance=1e-4, !1e-4 Saves some time compared to 1e-5
apply_rism_force=0, !Saves some time.
npropagate=1, !Saves some time and 4*8*Nbox bytes
ntwrism=1,
write_thermo=1,
/
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Jan 27 2016 - 02:30:04 PST
