Dear David,
The system is crambin, with 46 residues. The cubic water box is 12 angstrom.
The size_dipole_dipole_list printed in heat.out is 44526.
The result I pasted in the email is RMS FLUCTUATIONS, and the temperature
is well. I am sorry for the misunderstanding caused.
R M S F L U C T U A T I O N S
NSTEP = 9000 TIME(PS) = 9.000 TEMP(K) = 1.68 PRESS =
0.0
Etot = 41.1508 EKtot = 67.9002 EPtot =
68.8768
BOND = 39.4130 ANGLE = 33.7911 DIHED =
4.5198
1-4 NB = 13.2518 1-4 EEL = 0.0000 VDWAALS =
126.6247
EELEC = 88.1182 EHBOND = 0.0000 RESTRAINT =
0.0000
EPOLZ = 54.7209
Dipole convergence: rms = 0.166E-03 iters = 0.00
------------------------------------------------------------------------------
Maybe I should modify the "safety" parameter and see what is going on.
Best regards,
Ya Gao
On Wed, Oct 29, 2014 at 7:38 PM, David A Case <case.biomaps.rutgers.edu>
wrote:
> On Wed, Oct 29, 2014, Ya Gao wrote:
> > I performed a MD simulation under amoeba force field with
> pmemd.amoeba.MPI
> > in amber14.
> >
> > The minimization terminates normally. However, when the heat simulation
> > reached 9.0 ps, it was interrupted with the message " Too many
> > dipole_dipole interactions for allocated".
>
> I haven't seen this in a long time. How big is your system? What is the
> value of size_dipole_dipole_list (printed in the mdout file)? It seems
> quite
> odd that your temperature is still less than 2 K after 9 ps of simulation.
> Have you run other systems with amoeba?
>
> Since you have a trajectory with snapshots every 500 steps, I'd suggest
> first
> looking at that to see what is going on. A second step is to run a
> simulation with the serial version of pmemd.amoeba, to see if this might
> have
> something to do with the MPI code.
>
> Another thing to do is to Google "amber Too many dipole_dipole
> interactions for allocated", and try increasing the "safety" parameter as
> described there.
>
> If those steps don't help, you will probably have to post files that would
> allow someone else to reproduce the problem.
>
> ...regards...dac
>
>
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Received on Wed Oct 29 2014 - 06:00:05 PDT
