[gmx-users] simulation with non-zero total charge
seung43210 at yahoo.com
Sun Dec 13 15:29:50 CET 2009
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
--- On Fri, 12/11/09, Mark Abraham <Mark.Abraham at anu.edu.au> wrote:
> From: Mark Abraham <Mark.Abraham at anu.edu.au>
> Subject: Re: [gmx-users] simulation with non-zero total charge
> To: "Discussion list for GROMACS users" <gmx-users at 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:
> > DD cell 0 0 3: Neighboring cells do not have atoms:
> > 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
> -- gmx-users mailing list gmx-users at gromacs.org
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