From: Jim Phillips (jim_at_ks.uiuc.edu)
Date: Thu Nov 13 2003 - 15:52:31 CST
Hi,
In src/ComputeNonbondedUtil.C you would need to modify this piece of code,
which calculates the electrostatic potential function for cutoff
simulations (you can't do distance-dependent dielectric with PME).
case SPLIT_SHIFT: {
BigReal shiftVal = r2/cutoff2 - 1.0;
shiftVal *= shiftVal;
BigReal dShiftVal = 2.0 * (r2/cutoff2 - 1.0) * 2.0*r/cutoff2;
fast_energy = shiftVal/r;
fast_gradient = dShiftVal/r - shiftVal/r2;
scor_energy = scor_gradient = 0;
slow_energy = slow_gradient = 0;
}
break;
-Jim
On Mon, 10 Nov 2003, Sarah Harris wrote:
> Hello!!!
>
> I am hoping to use the Langevin dynamics option in NAMD to run some
> implicitly solvated, united atom simulations of aggregating proteins.
> The AMBER 84 parameters are specifically designed for a united atom
> representation, but require a linear distance dependent dielectric. The
> simulations that I wish to run are completely unfeasible in the presence
> of explicit water. Unfortunately, it does not appear to be possible to
> define distance dependent dielectric functions in NAMD - does anyone
> have any ideas? How difficult would it be to alter the source code to
> include this?
>
> I am also aware that the H-bonding interactions are defined differently
> for the 84 force-field (they are 10-12 rather than 6-12) but I was
> hoping to simply refit these parameters to the 6-12 interaction, which
> should overcome the problem. However, I cannot see a way around the lack
> of a distance dependent dielectric at present, but would very much
> appreciate any advice!!!
>
> Many thanks
> Sarah Harris
>
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