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?
(2) How can I fix this with "-rcon" option? I don't want to change LINCS order,
etc.
(3) Is there any parameter that I need to be careful when I simulate systems
with non-zero net charge (especially lipid system)?
Thank you very much for your advices!
Seunghwan Lee
University of North Carolina
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