Hi Jason,
________________________________________
From: Jason Swails [jason.swails.gmail.com]
Sent: Thursday, September 16, 2010 11:39 AM
To: AMBER Mailing List
Subject: Re: [AMBER] netCDF support for mmpbsa.py + general question
Hi Trevor,
On Thu, Sep 16, 2010 at 2:12 PM, Trevor Gokey <tgokey.mail.sfsu.edu> wrote:
> Hello,
>
> Is there any chance to have netCDF trajectory support for mmpbsa.py? I
> tried just adding netcdf to all the ptraj output, but since the final sander
> command gets sent to utils.py, I can't add the ioutfm=1 line in there.
> Sander is oh so much faster when reading binary.
>
I don't think we're going to add this. Ultimately we're going to move over
to NAB I think, when NAB gains the required functionality (decomposition)
and nab doesn't support netCDF. Also, the alanine scanning portion requires
ASCII crd files to operate. Lastly, how long is the trajectory reading
compared to the actual calculation? Does the entire trajectory file have to
get read in each time just to pull out one set of coordinate files (which
would be massively inefficient) or does it just read them as they need
them? You can add "ioutfm=1" to the gbmdin and pbmdin functions in utils.py
if you want, and then add the "netcdf" keyword at the end of the ptraj
output files in MMPBSA.py.
Ack, for some reason I though util.py was bytecode.... I made the change in util.py already.
I don't have hard numbers but when I changed all trajouts to include netcdf, I got huge speed ups which actually negated the need to run the mpi version. I say this because the mpi version bogged my PC and made it practically unusable (using openmpi 1.4.2 and latest mpi4py at the time of this writing). That being said, I'm glad you pointed me to edit util.py because converting my trajectories to ascii felt backwards.
However, we didn't really think the performance
increase of using netcdf warranted inclusion (since if coordinate reading is
the RDS, then it's pretty fast anyway ;) ).
> General question: how are the total energies calculated for the pb method?
> Gb looks straightforward because everything needed to calculate the total
> energy is listed in the final mmpbsa.py output. As for pb... an energy term
> that is used to calculate the final energy is missing from the total, or
> mmpbsa and I disagree on how to do general floating point arithmetic.
>
It's done in the same way that GB is. However, depending on your
"verbosity" setting, you can avoid printing a lot of redundant data. For
instance, for single-trajectory simulations, the bonded terms (including 1-4
interactions) must cancel or something has gone wrong. Therefore, they are
not printed by default (but they ARE checked for consistency and printed if
inconsistent). If they're not printed, they're subtracted from the reported
total. Only by setting verbose=2 in the input file will give you complete
agreement between the _MMPBSA_complex/receptor/ligand_pb.mdout files and the
final output file. Furthermore, G gas is the sum of the gas-phase terms
(VDWAALS, EEL, and the bonded terms if they're included) and G solv is the
sum of the solution phase terms (EPB and ECAVITY or EGB and ESURF for pb/gb,
respectively). Thus, all of the terms that come before the "total" should
add up to exactly twice the total, since that's what's added together. I
just checked it for amber11 by running the test files.
Now that I should have a functional patched netcdf version I should be able to see what verbose=2 gives me (in short time!). The reference to my question was the output given in your tutorial
http://ambermd.org/tutorials/advanced/tutorial3/py_script/section2.htm
The G gas and solv for pb don't match up with the total which was concerning because I was looking to post-process without the script. I'm assuming/hoping the energies will pan out when the verbosity is increased per your response. I was using the script from that tutorial.
Hope this helps,
Jason
Helps a lot. Thanks.
Trevor
>
> Thank you,
> Trevor Gokey
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Sep 16 2010 - 14:00:04 PDT
