VMD-L Mailing List

From: Tim Lo (timlo_at_hku.hk)
Date: Fri Feb 14 2014 - 09:23:50 CST

Hi Javad,

Please be careful of the shape of the solvent box too. The
pre-equilibrated box should be cubic in order for VMD Solvate to run
properly. When you perform equilibration of your solvent box, you should
set the three cell basis vectors of the Periodic Boundary Conditions to
be the same.

Regards,
Tim

On 2014/2/14 ?? 08:47, Norman Geist wrote:
>
> VMDs solvate GUI is able to handle non standard solvent. All you need
> is a pre-equilibrated box with pdb/psf and its topology.
>
> Norman Geist.
>
> *Von:*owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] *Im
> Auftrag von *Javad Noroozi
> *Gesendet:* Freitag, 14. Februar 2014 12:59
> *An:* namd-l_at_ks.uiuc.edu
> *Betreff:* namd-l: Solvation in non standard solvent
>
> How can solvate a drug in non standard solvent using NAMD?
>
> Javad Noroozi
>
> Chemical Engineering Department
>
> Sharif University of Technology
>
> Email: jnoroozi_at_che.sharif.ir <mailto:jnoroozi_at_che.sharif.ir>
>
>
>
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