VMD-L Mailing List

From: Peter Freddolino (petefred_at_umich.edu)
Date: Wed Aug 02 2017 - 10:35:08 CDT

Dear Sebastien,
Given where that message is occurring, I suspect that your vmd may have
been built without multithreading support. Could you confirm what
version you are running and how you installed it?
Thanks,
Peter

On 08/02/2017 07:00 AM, Sebastian Reiter wrote:
> 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
>>>