Hi David,
It won't work with any pmemd tests in the test suite. The following is from
the 4096wat test output. The same thing happens. It seems to me that
pmemd.MPI somehow messed up electrostatic interactions. The vdwaals
(6028.9517) is identical with the sander output though.
NSTEP = 1 TIME(PS) = 1.001 TEMP(K) = NaN PRESS =
0.0
Etot = NaN EKtot = NaN EPtot =
NaN
BOND = 0.0000 ANGLE = 0.0000 DIHED =
0.0000
1-4 NB = 0.0000 1-4 EEL = 0.0000 VDWAALS =
6028.9517
EELEC = NaN EHBOND = 0.0000 RESTRAINT =
0.0000
Ewald error estimate: NaN
On Thu, May 24, 2018 at 5:38 AM, David A Case <david.case.rutgers.edu>
wrote:
> On Wed, May 23, 2018, Hai Long wrote:
> >
> > We recently upgraded from Amber14 to Amber18. The compiler, MPI, and MKL
> > that I used for Amber 18 are all intel 2017.0.5. The sander, sander.MPI,
> > and serial pmemd are all working properly. However, pmemd.MPI produces
> > errors. The following output is from a simulation of a 5X5X5nm
> equilibrated
> > water box, showing something wrong with EELEC and VIRIAL:
>
> Thanks for the report. We would need to see the actual inputs, plus the
> command-line options you chose, in order to try to track down the
> problem. It looks like there is something wrong with your input
> coordinates.
>
> (I'm assuming that you have run the pmemd test suite in parallel, and
> that things look OK there. If you haven't done this, please do so,
> since that can remove the possibility of a bad input file.)
>
> ....dac
>
>
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Received on Thu May 24 2018 - 15:00:02 PDT
