From: Sebastian Reiter (
Date: Wed Aug 02 2017 - 14:58:58 CDT

Dear Peter,

I am using version 1.9.3 of vmd, specifically the binary distribution
LINUX_64 OpenGL, CUDA, OptiX, OSPRay (Linux (RHEL 6.7 and later) 64-bit
Intel/AMD x86_64 SSE, with CUDA 8.x, OptiX, OSPRay). I installed it by
running configure with the standard options given below, followed by
make install.


Also, the startup message of vmd indicates that multithreading is available:

> Info) Multithreading available, 4 CPUs detected.
> Info) CPU features: SSE2 AVX AVX2 FMA

Best regards,

Am 02.08.2017 um 17:35 schrieb Peter Freddolino:
> 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