VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu Jul 05 2018 - 15:09:01 CDT

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/