[gmx-users] adding water with genbox

[Mark Abraham]

Hi,

Also you can use pressure coupling to shrink a box to then use as a
solvated box.

Mark

On Fri, 29 Jan 2016 22:55 Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> 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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