VMD-L Mailing List

From: Peter Freddolino (petefred_at_umich.edu)
Date: Fri May 17 2019 - 12:01:23 CDT

Dear San,
This issue had been brought up a little while ago (
https://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/28784.html) - the
answer is that multithreading in the CPU version was disabled to make it
compatible with the multilevel summation code. Speaking of that -- unless
you have a very good reason to be doing this with a brute force
calculation, things will run much faster if you use multilevel summation
(add "-m multigrid" to the command line arguments).
Best,
Peter

On Fri, May 17, 2019 at 12:29 PM san kumar <ksan93259_at_gmail.com> wrote:

> Dear VMD users,
>
> I am using cionize plugin (version 1.0) in the new version of VMD (1.9.4).
> The capsid net charge is -240e. The calculation is running for 10 days and
> is not still completed. I am using following command:
>
> *cionize -i cionize.in <http://cionize.in> -p 4 capsid.pqr*
>
> The calculation is not running parallel. Please see the below message:
>
> Number of atoms: 915960
> Number of grid points: 362422340
> Calculating grid energies...
> calc_grid_energies_excl_jsthr()
>
> *using 1 processors*
>
> Any kind of advice/suggestions will be deeply appreciated.
>
> Thanks in advance,
> San
>