VMD-L Mailing List

From: Peter Freddolino (petefred_at_umich.edu)
Date: Tue Aug 01 2017 - 22:01:30 CDT

Dear Sebastian,
Can you confirm how you generated the structure you loaded into vmd? In
particular, are the charges set properly? I suspect that they are not
loaded given the output that you indicate that you have; for example,
you may have forgotten to load a psf file.

Could you post the output from your job to clarify at which point the
use of only one processor was reported?

Best,
Peter

On 08/01/2017 03:57 PM, Sebastian Reiter wrote:
> Dear all,
>
> I am trying to use the cionize plugin (version 1.0) in vmd 1.9.3 to
> neutralize the charges of an RNA backbone. So far, I have found out how
> to start the plugin and the following exemplary command does not yield
> an error message:
>
> cionize -mol 0 -mg -np 4 -go potential.dat -ions "{SOD 85 1}"
>
> However, the output shows that only one processor was used despite the
> option "-np 4" and, more importantly, the generated ions are just placed
> cubically around the RNA structure. A quick look into the output file
> "potential.dat" shows that cionize sets the potential to zero at every
> grid point.
>
> I would greatly appreciate your advice on how to use cionize correctly,
> so that I can make use of the parallel implementation and the ions are
> placed in sensible positions.
>
> Best regards,
> Sebastian
>