Replying to list for the record (I sent structs and inputs to Tyler and
Dave so they could have a look, some helpful discussion followed).
1) 3D RISM energies can be very sensitive to conformation, especially at
high concentrations of multiple species in the solvent, and especially with
cavities or odd-shaped surfaces in the solute. This is not entirely a bad
thing and might be at least somewhat physical, but is a pitfall when doing
single-point energy evaluation of structures generated with other means
such as GBSA.
2) Sampling with MD-RISM is manageable and avoids massive jumps in energy:
the potential surface described is at least somewhat smooth in the
valleys. If minimisations or singlepoint energy evaluations are behaving
suspiciously, my takehome from this is to just pick the lowest-energy snap
and do MD from it as a starting point.
I got (apparently) adequate results using this input file, simplified
somewhat from the one in the manual as I wanted to avoid multiplying my
problems with too much novelty:
comment here
&cntrl
ntx=1, ntpr=10, ntwx=10, ntwr=10, nstlim=2000, dt=0.001,
ntt=3, tempi=300, temp0=300, gamma_ln=10., ig=3233, !Langevin MD
ntb=0,
!Non-periodic
cut=999., !solute-solute interactions
irism=1,
/
&rism
rismnrespa=2,
fcestride=0,fcecrd=2,
/
"RISM! You have it or you don't, that's a fallacy" .... Gorrillaz, Clint
Eastwood.
Josh
On 27 January 2016 at 11:05, Josh Berryman <the.real.josh.berryman.gmail.com
> wrote:
> 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,
>
> /
>
>
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Received on Mon Feb 01 2016 - 05:30:04 PST
