VMD-L Mailing List

From: Christopher Gillespie (gillescche_at_gmail.com)
Date: Mon Jul 28 2008 - 07:33:37 CDT

Hello Sue,
I don't want to supply my possibly naive interpretation of padding so I will
leave that to the more informed, but I can comment on your other questions.

Here is an example script I have used to solvate my protein with a specific
box size

============================
resetpsf

readpsf Protein.psf

coordpdb Protein.pdb

mol load psf Protein.psf pdb Protein.pdb

package require solvate
solvate Protein.psf Protein.pdb -b 4.0 -t 20 -minmax {{-10 -10 -10} {10 10
10}} -o solvate
=================================

To measure your actual box dimensions, use measure minmax in VMD.

I believe both of these are touched on in the tutorial for ubiqutin(sp?).

Best

Chris

On Mon, Jul 28, 2008 at 2:25 AM, Sue Legge <sue.legge_at_rmit.edu.au> wrote:

> A couple of questions regarding solvating a peptide in a cubic box with
> periodic boundary conditions,
>
> what exactly is the padding?
>
> is it possible to specify an exact box size? Eg. can I create a box
> 50x50x50 angstrom?
>
> also, is there some way to measure the exact size of the box?
>
> thanks
> sue
>
> ____________________
> Fiona Sue Legge, PhD
> Applied Physics
> School of Applied Sciences
> Science, Engineering and Technology Portfolio
> GPO Box 2476V
> Melbourne, 3001
> Australia
>
> phone: +61 3 9925 9555, 9208 4287
> fax: +61 3 9925 5290
> email: sue.legge_at_rmit.edu.au
> __________________________
> IMPORTANT NOTE
> This email and any attachments are confidential and subject to copyright.
>
> If you have received this e-mail in error, please immediately notify the
> sender by reply email and remove and destroy any copies of this email and
> any attachments. If you are not the intended recipient you are hereby
> notified that any disclosure, copying, transmission or other use of this
> email and any attachments is unauthorised and strictly prohibited.
>
>
>
>