Mark, Thanks for your comments. Well, I am running simulations with or without neutralization to see the effect of counter ions. The troubling simulations have messages like
> 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% during the simulation and it has pretty big load imbalance. I am wondering what is the meaning of "minimum cell size" in DD and how I can change it manually. Seunghwan Lee --- On Fri, 12/11/09, Mark Abraham <mark.abra...@anu.edu.au> wrote: > From: Mark Abraham <mark.abra...@anu.edu.au> > Subject: Re: [gmx-users] simulation with non-zero total charge > To: "Discussion list for GROMACS users" <gmx-users@gromacs.org> > Date: Friday, December 11, 2009, 5:12 PM > 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 > -- gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use > the www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php