From: Jim Phillips (jim_at_ks.uiuc.edu)
Date: Thu Sep 20 2012 - 18:39:27 CDT

How often are you regenerating angles and dihedrals? There is no reason
to do this more than once at the end. Psfgen only marks
atoms/bonds/angles/dihedrals/etc as deleted. It doesn't actually unlink
them until you call resetpsf (or delete the context with psfcontext). If
you repeatedly regenerate angles and dihedrals you have to walk through
every angle and dihedral that ever existed.

-Jim

On Thu, 20 Sep 2012, John Stone wrote:

> Hi,
> There isn't a parallel version of psfgen presently. I think the longest
> psfgen run I'd heard of previously was about a half-day for a 100 million
> atom system, including solvent box generation. If yours took over 5 days,
> then I'd have to say that it sounds like some of your structure building
> steps are driving psfen in a much less optimal way than expected. If you
> have a structure building script that you would be willing to give us to
> use to test with, we can research improving the performance of whatever
> psfgen step(s) are most responsible for the long build time you describe.
>
> Your runtimes are so much slower than what we'd seen before, that I suspect
> you're triggering some psfgen behavior that either hasn't been optimized,
> or that has some particularly bad algorithmic performance. Before we would
> even start thinking about parallelizing psfgen, I would first like to be
> sure that all of the algorithmic components are no worse than linear time
> in your particular case. I suspect you have found a combination of psfgen
> build steps that are resulting in quadratic runtime of one or more of the
> psfgen internal algorithms, and in a case we had not run into previously.
> Let us know if you're willing to give us a copy of your files and build
> scripts so we can reproduce the performance problem you describe.
>
> Cheers,
> John Stone
> vmd_at_ks.uiuc.edu
>
> On Thu, Sep 20, 2012 at 05:25:29PM -0500, Ganesh Kamath wrote:
>> Hi John,
>> It took about 5-6 days for this system to build. The primary reason was
>> that I use patch to stitch the monomers of the polymer, the regenerate
>> angle and dihedral is memory intensive. Finally the water box of around 2
>> million molecules just took half a day.
>> Is there a parallel version of psfgen?
>> I am still making tests on the system.
>> Cheers,
>> Ganesh
>>
>> On Sep 20, 2012 5:08 PM, "John Stone" <johns_at_ks.uiuc.edu> wrote:
>> Hi,
>> I don't recall if anyone replied to this, and I was out sick for a
>> few days after your email, but it is easy to write a .js file from
>> a given PSF/PDB pair by making an "all" atom selection and doing:
>> $sel writejs filename.js
>>
>> If your structure gets too large for psfgen to handle, you'll either
>> need to use the standalone version of psfgen that can write js files
>> directly, or I can make a special build of VMD for you that includes
>> a psfgen plugin that knows how to work with the js files. Eventually
>> this will be the standard version of psfgen shipped with VMD, but
>> I can't switch over to it until we get a few issues resolved for the
>> Windows version of VMD/psfgen.
>>
>> Cheers,
>> John Stone
>> vmd_at_ks.uiuc.edu
>>
>> On Fri, Sep 07, 2012 at 09:57:39AM -0500, Ganesh Kamath wrote:
>> > Hi Folks,
>> > I have a syste...
>>
>> --
>> NIH Resource for Macromolecular Modeling and Bioinformatics
>> Beckman Institute for Advanced Science and Technology
>> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
>> http://www.ks.uiuc.edu/~johns/ Phone: 217-244-3349
>> http://www.ks.uiuc.edu/Research/vmd/ Fax: 217-244-6078
>
> --
> NIH Resource for Macromolecular Modeling and Bioinformatics
> Beckman Institute for Advanced Science and Technology
> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> http://www.ks.uiuc.edu/~johns/ Phone: 217-244-3349
> http://www.ks.uiuc.edu/Research/vmd/ Fax: 217-244-6078
>