VMD-L Mailing List

From: Mani Kandan (manikandand5110_at_gmail.com)
Date: Thu Jul 05 2018 - 09:50:31 CDT

Hi,

       By using inorganicbuilder, creating substrate and adding bonds takes
nearly 7 hours. Solvating takes 2 to 3 hours depending upon size of
reservoir and autoionize takes 2 to 3 days.

Thanks,

Manikandan

On Thu, Jul 5, 2018, 7:39 PM John Stone <johns_at_ks.uiuc.edu> wrote:

> Hi,
> If your performance issue only involves the use of "solvate" and
> "autoionize" then there's unlikely to be any benefit from running
> VMD in parallel. How long are your system preparation steps taking?
> I wouldn't expect a 10 million atom system to be much of a challenge.
>
> Best,
> John Stone
> vmd_at_ks.uiuc.edu
>
> On Wed, Jul 04, 2018 at 12:12:21AM +0530, Mani Kandan wrote:
> > Dear all,
> >
> > My system has 10 million atoms, solvating my system takes more
> > time and for autoionize too. For that purpose, I want to run in parallel.
> > Is it possible? Or Is any other way?
> >
> >
> > Manikandan
>
>
> --
> 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/
>