VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu May 26 2016 - 12:32:21 CDT

If you prepare a template solvent box, it is possible to use the
"solvate" plugin with custom solvent boxes, as well as the standard
water box it builds by default. See the documentation for the solvate
plugin for more information. Also, if the solvate plugin doesn't do
what you want, then you would likely want to use "psfgen" to prepare the
structure which is more involved but allows greater control.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Thu, May 26, 2016 at 05:22:45PM +0000, Deng, Jinxia (Nancy) wrote:
> Hi all,
>
>
>
> I would like to set up peptide simulations by NAMD in various single
> solvent environment, such as water, DMSO, etc.
>
>
>
> Wonder whether VMD can do this. If so, can anyone share any tutorial??
>
>
>
> If not, can anyone advise me a place to start??
>
>
>
> Regards,
>
>
>
> Nancy 

-- 
NIH Center for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
http://www.ks.uiuc.edu/~johns/           Phone: 217-244-3349
http://www.ks.uiuc.edu/Research/vmd/