[gmx-users] adding water with genbox

[Justin Lemkul]

On 1/29/16 4:16 PM, Irem Altan wrote:
> Hi,
>
> I am using gromacs 4.6, so I still use genbox to solvate the protein I’m simulating. How does genbox adjust the density? I am trying to pack water molecules in a tight protein unit cell, and genbox is having problems packing enough water molecules for the water density to be ~1g/cm^3. If I modify vdwradii.dat to shrink the radii a little bit, does that affect the maximum density that the solvent can have? In other words, will genbox add as many water molecules as it can if the radii are small enough, or will it stop when d=1g/cm^3?
>

genbox takes the input (presumably equilibrated) solvent configuration and tiles 
it through the unit cell while using the van der Waals radii to avoid atomic 
clashes.  It doesn't use any density information directly.  The new solvate 
module (5.0 and newer) has a -scale option that can modulate this to an extent, 
but keep in mind (1) as soon as you equilibrate, everything changes and (2) 
perhaps more importantly, most water models don't actually give the exact 
density of water, anyway.

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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