Hi Amber users,
I see the following error message occurring seemingly at random (in about
20% of runs) in some repeats of a large membrane system simulation (running
Amber22 pmemd.CUDA on RHEL with ff19SB+gaff2+lipid21+OPC water):
-----------------------------------------------
ERROR: Calculation halted. Periodic box dimensions have changed too much
from their initial values.
Your system density has likely changed by a large amount, probably from
starting the simulation from a structure a long way from equilibrium.
[Although this error can also occur if the simulation has blown up for
some reason]
...
------------------------------------------------
A quick search shows this message related to badly equilibrated systems,
but my case looks quite stably equilibrated and neither the density nor
periodic box change much (certainly less than 5%) during the simulations.
Nothing I see in the output or any other error messages suggest the system
is blowing up (no vlimit errors or so). I havent looked into the code in a
long time, does anyone know what exactly has gone wrong that caused pmemd
to halt?
I use SHAKE, 2fs timestep, Langevon thermostat, berendsen (because of the
lipid issue with MC) barostat with taup=2 and ntb=2, cutoff = 10.
Nothing else is odd about the system, no extra forces, custom parameters,
odd chemistry or anything weird, just a pretty large protein in a membrane
with ca 100k particles total.
Has anybody seen similar cases or any ideas what (if anything) I may be
doing wrong here?
Since the crashes/exits appear randomly, I assume they will not happen when
I restart, but this a) costs time, b) needs human monitoring of long runs
and c) makes me wonder if my settings are not suited for long membrane
simulations somehow.
Kind Regards,
Thomas
--
*Dr. Thomas Steinbrecher*
Principal Scientist CADD
Roche Pharma Research and Early Development
Roche Innovation Center Basel
F. Hoffmann-La Roche Ltd
Bldg. 092/3.92
Grenzacherstrasse 124
4070 Basel
Switzerland
Phone +41 61 682 1319
mailto: thomas.steinbrecher.roche.com
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon May 15 2023 - 01:30:02 PDT
