As an update to this, I'm finding some weird timings with PB when run
through our script. Below is the input file being printed by our
script, so maybe someone more familiar with PBSA can enlighten me as
to which variables I am setting that is killing the performance.
Here is the input file:
File generated by MMPBSA.py
&cntrl
ntb=0, cut=999.0, nsnb=99999,
imin=5, maxcyc=0, cutcap=-1, xcap=0,
ycap=0, zcap=0, idecomp=0, ntpr=1,
ivcap=0, ntmin=2, igb=10, ipb=1, inp=1,
/
&pb
dbfopt=1, epsin=1, epsout=80, istrng=100.0,
radiopt=0, sprob=1.4, space=0.5, maxitn=1000, npopt=1
cavity_surften=0.00542, cavity_offset=-1.008,
fillratio=4,
/
When istrng is set to 0, this will finish 1 frame in 1.613 minutes.
When istrng is 100.0 (mM), 1 frame takes 20.057 minutes (I'm not sure
which revision this started happening in, but it's relatively recent).
When I find out what I should change above, I will send the patch for
utils.py that also has the fix for utils.which.
Thanks!
Jason
On Mon, Mar 29, 2010 at 4:46 PM, Jason Swails <jason.swails.gmail.com> wrote:
> Hello,
>
> I've fixed "utils.which" so that it will look for each program in
> $AMBERHOME/exe if it can't find it in PATH. I'm working on the other
> problem now (but you are right, it's not a short test and I'm guessing
> I'll be getting the same error). I believe it has to do with the fact
> that the input file we create in MMPBSA.py is no longer compatible
> with the current version of PBSA. When we get that fixed, I'll send a
> patch for utils.py (which should fix both problems). I can also re-do
> the test slightly so it takes far less time and tests GB/PB
> separately.
>
> Thanks!
> Jason
>
> On Mon, Mar 29, 2010 at 3:29 PM, case <case.biomaps.rutgers.edu> wrote:
>> On Mon, Mar 29, 2010, Jason Swails wrote:
>>>
>>> utils.which does indeed search through PATH (not a standard python
>>> function). Should it instead depend on AMBERHOME being present?
>>
>> The tests are all over the place in this regard, but a great many require
>> AMBERHOME to be set correctly, and the manual says to do this. So,
>> utils.which should search in $AMBERHOME/bin, and *not* in PATH.
>>
>> (I put the next problem in a separate email.)
>>
>> ...thx...dac
>>
>>
>> _______________________________________________
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>> AMBER-Developers.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber-developers
>>
>
>
>
> --
> ---------------------------------------
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Graduate Student
> 352-392-4032
>
--
---------------------------------------
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Mon Mar 29 2010 - 16:30:02 PDT
