Re: [AMBER] About difference between Sander and Pmemd

From: Robert Duke <>
Date: Thu, 16 Jun 2011 20:10:51 -0700

I am not sure what the exact differences observed really are, or what the
simulation timeframes are (sorry, I have not been following this closely).
However, let me make several points: 1) simulations on multiple processors
typically start visibly diverging (ie., in observed energies in the mdout
file) in around 500 steps, due to rounding errors associated with the order
of force additions (something that is nondeterministic due to indeterminacy
of network packet delivery order), and 2) there IS a difference in how pmemd
and sander define molecules in some systems. Sander trusts the prmtop to be
correct, and takes it's molecular definition from the prmtop, even if the
prmtop defines two molecules that are covalently bonded. In
wrapping/reimaging, sander will wrap the two covalently bonded "molecules"
as if they were not joined, sometimes with not the best results. PMEMD, on
the other hand, examines the prmtop data to insure no covalent bonding
between molecules. If bonding is discovered, pmemd will by default redefine
this as one molecule, and treat it as a single unit in wrapping. This is
technically more correct and less troublesome. There is also a slight
effect on virial computations in all this. If memory serves, I think I
first introduced this difference to handle a complexity associated with the
definition of frames of reference for extra points when a forcefield
requiring extra points is used, but I made it the default because it created
LESS grief in wrapping molecules. It is possible to override this
behaviour, if memory serves, with the no_intermolecular_bonds namelist
variable (sorry, I don't have source or manuals up anywhere at the moment,
so this is all off the top of my head, and I have not thought about it in a
long while). Anyway, there are several possible sources of differences,
especially in wrapping. When I used to run long simulations, I was pretty
careful about when I did wrapping, especially if I had a collection of
molecules that were not covalently bonded that I wanted to keep together.
All this may not apply to your simulation; I know not, but thought I would
make a note of some known differences.
Regards - Bob Duke

----- Original Message -----
From: "Bin Wu" <>
To: "AMBER Mailing List" <>
Sent: Thursday, June 16, 2011 6:24 PM
Subject: Re: [AMBER] About difference between Sander and Pmemd

> 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.
> 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 <>
>> 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
>> _______________________________________________
>> AMBER mailing list
> _______________________________________________
> AMBER mailing list

AMBER mailing list
Received on Thu Jun 16 2011 - 20:30:03 PDT
Custom Search