Re: setting solvent density during solvation

From: Cesar Luis Avila (cavila_at_fbqf.unt.edu.ar)
Date: Mon Aug 20 2007 - 14:46:01 CDT

Dear Adam,
I think that the solvation box was built with a rather low density to
avoid getting high VdW forces when building the system. You are expected
to run a few equilibration steps using NPT until you get to the desired
density. Then you can switch to the ensemble you want to use.
Hope this helps
Cesar

Adam Fraser escribió:
> I was wondering if there is a way to specify a solvation density of
> 1.0 (rather than 0.93) using vmd.
>
> This is the script I'm currently using in vmd:
>
> resetpsf
> readpsf 2HEX.psf
> coordpdb 2HEX.pdb
> resetpsf
> package require solvate 1.2
> solvate 2HEX.psf 2HEX.pdb -o 2HEX_solv2 -s WT -b 2.4 -minmax { {-7.5
> -12.5 -12.5} {47.5 12.5 12.5} }
>
> Any help or suggestions would be great. Thanks,
> Adam

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 05:20:32 CST