From: Mani Kandan (manikandand5110_at_gmail.com)
Date: Thu Jul 05 2018 - 21:03:55 CDT

Yes, I am using latest version vmd 1.9.4.a.

Manikandan

On Fri, Jul 6, 2018, 1:39 AM John Stone <johns_at_ks.uiuc.edu> wrote:

> I forgot to ask another important question, what version of VMD
> are you using? These tools depend on 'psfgen' and the performance
> of 'psfgen' was improved significantly in recent versions vs. the past,
> so I want to make sure you're running a current VMD build before we
> dig much further into what you're doing here.
>
> Best,
> John Stone
> vmd_at_ks.uiuc.edu
>
> On Thu, Jul 05, 2018 at 08:20:31PM +0530, Mani Kandan wrote:
> > 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/
> > >
>
>
> --
> 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/
>