On Thu, Jun 16, 2011 at 7:24 PM, Bin Wu <wubin2002.gmail.com> wrote:
> Thank you very much for your reply.
>
> I am pretty sure that my simulation results obtained from Sander and Pmemd
> are different. The evident difference would be the bond breaking phenomena
> in Pmemd which are absent in the case of Sander.
>
Bonds can't *really* break. They can _appear_ to break due to some
visualization artifacts (see Bob's discussion regarding wrapping, etc.), but
they can't actually break. Since there can be such a large discrepancy
between what is actually happening and what appears to be happening, we'd
need more than just a description of what is (or simply appears to be)
happening.
Also, you can never compare 2 long simulations (even 2 long pmemd
simulations with the same random seed and starting points) due to the
dynamic load balancing that will cause simulations to diverge. The best you
can do is compare ensemble properties, and check to make sure that these are
consistent.
HTH,
Jason
> As for the previously mentioned "Permission denied" while I launched "make
> test.pmemd", I figured out the problem was that the test script was not set
> as executable. After I enabled them as executables, the test process went
> on
> without any trouble. And I looked into the test cases showing "Possible
> failure", there are only very subtle differences between the simulation
> results got from my machine and the references, which make me believe they
> are just rounding errors.
>
> I am very confused. Since my installation could pass those test, does not
> that mean I install pmemd correctly? And if that is true, why my simulation
> results from Sander and Pmemd are so different?
>
> I would be very grateful if someone can help me with this issue.
>
> Thank you very much for your attention.
>
> Best Regards!
>
> Bin
>
>
> 2011/6/16 David A Case <case.biomaps.rutgers.edu>
>
> > On Wed, Jun 15, 2011, Bin Wu wrote:
> > >
> > >
> > > Therefore, I wonder simulation results from Pmemd and Sander are
> supposed
> > to
> > > be different
> >
> > Sander and pmemd should give identical results; indeed, the test cases
> for
> > pmemd are the same as those for sander, just running a different
> > executable.
> > But be sure to read section 1.3.4 of the Users' Manual, which discusses
> > numerical differences between programs.
> >
> > Check your visualization to be sure there is not some imaging problem.
> Of
> > course, it is also possible that you have uncovered some bug. Check the
> > coordinates of atoms that should be bonded to be sure they have indeed
> > separated.
> >
> > > or I compiled Pmemd wrong, because the process of Pmemd
> > > installation is not smooth at all.
> >
> > Details would help. Compiling pmemd is supposed to be completely smooth
> > (always is for me). But there are an enormous number of combinations of
> > compilers and operating systems, so we need to know details of what went
> > wrong.
> >
> >
> > >
> > > export TESTsander='../../../../exe/pmemd'; cd chamber/md_engine/dhfr &&
> > > ./Run.dhfr_charmm.min
> > > /bin/sh: ./Run.dhfr_charmm.min: Permission denied
> > > make: *** [test.pmemd] Error 126
> >
> > This is odd, and I do not recall seeing such a message before. Check the
> > permissions on the file involved: is it indeed executable? What happens
> if
> > you try to execute that script by hand?
> >
> > ....dac
> >
> >
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--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Fri Jun 17 2011 - 00:00:05 PDT
