VMD-L Mailing List

From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Thu Jun 28 2007 - 12:00:13 CDT

Hi Amit,
it's now possible to use solvate for nonwater solvents once you have a
small equilibrated box (see
http://www.ks.uiuc.edu/Research/vmd/plugins/solvate/). To make that
initial box, I'd just recommend making a pdb file that has (say) 500
glycerol molecules, and then randomize their coordinates in VMD (just by
translating them) and equilibrate that box with an NPT simulation. You
can then use solvate to create whatever type of box you need.
Peter

amit dong wrote:
> Hi VMD community.
>
> I need to a make a box of gycerol molecules. I have with me
> coordinates for 1 gycerol, its parameter file and the topology file.
> How do I go about doing this? Do I need to tweak the solvate script or
> is there any easier method.
>
> Any help will be much appreciated.
> Thanks
> Amit
>
>