[gmx-users] simulation with non-zero total charge
Mark.Abraham at anu.edu.au
Mon Dec 14 02:08:59 CET 2009
seunghwan lee wrote:
> 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
See manual 3.17
> --- 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:
>>> 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
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