Thank you so much for your replies.
I minimized the system first then throw the minimized structure into the
pmemd simulation. Subsequently the observed "bond breaking" like phenomenon
is gone.
Thank you very much.
Bin
2011/6/17 Jason Swails <jason.swails.gmail.com>
> 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 - 07:30:03 PDT
