[gmx-users] simulation with non-zero total charge

seunghwan lee seung43210 at yahoo.com
Fri Dec 11 22:29:22 CET 2009


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


More information about the gromacs.org_gmx-users mailing list