VMD-L Mailing List

From: Sebastian Reiter (reiter.se_at_t-online.de)
Date: Tue Aug 01 2017 - 14:57:23 CDT

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