From: Ana Celia Vila Verde (acavilaverde_at_gmail.com)
Date: Tue Jun 03 2014 - 06:29:02 CDT
The reduction in volume that you see during equilibration is normal;
after the equilibration the water will have the correct density, which
is what you want. If you prefer a 10 A water cube, use solvate.tcl to
create a 11 A cube; after equilibration it should have an edge length
close to 10 A.
Keep in mind, though, that if your water cube has an edge that's 10 A
then you need a cutoff for the non-bonded interactions of no more than 5
A. This will not work well because most water force-fields were
parameterized with cutoff distances of order 9 to 12 A. This means that
simulation boxes should not have edge lengths smaller than 18 to 24 A
(twice the cutoff length).
I hope this helps,
On 03/06/14 12:22, Akshay Bhatnagar wrote:
> I want to create a 10 A water cube but whenever i use the solvate.tcl
> script to do the same the density of the box deceases due to which the
> same of box is deformed in equilibration and production run.
> can anyone help me please?
> With Regards
> Akshay Bhatnagar
> PhD Student
> BITS Pilani Hyderabad Campus
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