VMD-L Mailing List

From: Sebastian Reiter (reiter.se_at_t-online.de)
Date: Wed Aug 02 2017 - 06:00:46 CDT

Dear Peter,

thank you very much for your quick and helpful reply. You are right: I
did not load a psf file, so the charges were missing. Loading the psf
fixed the error and the ion positions look reasonable now.

In the output, the input parameters are reported correctly at the very
beginning:

> Running cionize on input file cionize-temp.pqr
> Ion-solute distance: 6.000000
> Ion-Ion distance: 10.000000
> Grid spacing: 0.500000
> Boundary size: 10.000000
> Max. Processors: 4

However, when the actual calculation starts, it does not seem to be
running in parallel, which I could also confirm by looking at the system
load:

> Calculating grid energies...
> Multilevel summation for electrostatic potential map
> using 1 processors

The same happens, when double precision is used instead of multilevel
summation.

Best regards,
Sebastian

Am 02.08.2017 um 05:01 schrieb Peter Freddolino:
> 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
>>
>