seunghwan lee wrote:
Hi,
I am trying to simulate lipid bilayer with protein, which has net positive
charge. If I run simulations after neutralizing, I don't have any problem,
whether I use PME or reaction-field. But, when I try to run it with net
positive charge using reaction-field, I got domain-decomposition error
after 1800000 steps. In log file, I have
DD load balancing is limited by minimum cell size in dimension Z
DD step 1878999 vol min/aver 0.840! load imb.: force 18.6%
and the actual error message was
DD cell 0 0 5: Neighboring cells do not have atoms: 4484
DD cell 0 0 3: Neighboring cells do not have atoms: 4477
-------------------------------------------------------
Program mdrun, VERSION 4.0.5
Source code file: domdec_con.c, line: 679
Fatal error:
DD cell 0 0 5 could only obtain 51 of the 52 atoms that are connected via
constraints from the neighboring cells. This probably means your constraint
lengths are too long compared to the domain decomposition cell size. Decrease
the number of domain decomposition grid cells or lincs-order or use the -rcon
option of mdrun.
My questions are:
(1) Is this error anything to do with the fact that the system has net charge?
Potentially. Something's causing it to explode, but it can be hard to
tell why after the fact.
(2) How can I fix this with "-rcon" option? I don't want to change LINCS order,
etc.
Reading mdrun -h is the first port of call, however changing this option
is probably just fixing the symptoms, not the cause.
(3) Is there any parameter that I need to be careful when I simulate systems
with non-zero net charge (especially lipid system)?
With RF, I would have guessed that there's probably not much to worry
about. Probably nobody's studied it in any detail, because it's so easy
to neutralize, and so easy to defend a neutral simulation as a realistic
model of real physics...
Mark
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