[gmx-users] X particles communicated to PME node Y are more ...

[Justin Lemkul]

On 3/4/13 3:08 PM, Miguel Ángel Mompeán García wrote:
> I have tried the same issue (same system with same mdp file and same
> initial configuration as starting structure) and is running without
> any problems with GROMACS-4.5.5.
>
> Anyone knows what is happening?
>

You didn't tell us your Gromacs version in the previous post so the best guess 
is "random bug that was somehow fixed before 4.5.5."

-Justin

>
> 2013/3/4, Justin Lemkul <jalemkul at vt.edu>:
>>
>>
>> On 3/4/13 8:25 AM, Miguel Ángel Mompeán García wrote:
>>> Dear gmx users,
>>>
>>> I have successfully performed simulations on a charged peptide. I did a
>>> series of mutations and everything had a happy end. Now I have tried
>>> another mutation (just substitution of Asn to Lys) and I am getting the
>>> well-known
>>>
>>> "X particles communicated to PME node Y are more than a cell length out
>>> of
>>> the domain decomposition cell of their charge group"
>>>
>>> message error during energy minimization, right at the beginning (step
>>> 0).
>>>
>>> My energy minimization mdp file looks as follows:
>>>
>>>
>>> integrator      = steep         ;
>>> emtol           = 1000.0        ;
>>> emstep          = 0.02          ;
>>> nsteps          = 70000         ;
>>> nstlist         = 1                   ;
>>> ns_type         = grid            ;
>>> rlist           = 1.0                   ;
>>> coulombtype     = PME       ;
>>> rcoulomb        = 1.0            ;
>>> rvdw            = 1.0               ;
>>> pbc             = xyz                ;
>>>
>>>
>>> I have tried without neutralizing with ions, changing the time step,
>>> changing the integrator and the values for rcoulomb,rlist, etc.
>>
>> Bad idea.  Nonbonded cutoffs are an intrinsic part of the force field.
>> Changing
>> them will actually increase your likelihood of failure.
>>
>>> I have changed all the parameteres in the mdp file and I get a smaller
>>> value of particles in the message error, but still a crash.
>>> The box size has also no effect on the message error.
>>> I have checked the starting structure and everything is fine. Mutating
>>> that
>>> Asn to a non-charged residue does not yield any problem, but I want to
>>> study the effect in the Asn--> Lys mutation.
>>>
>>> Any hint to solve the error?
>>>
>>
>> If EM stops at the first step, there's usually something catastrophically
>> wrong
>> with the starting configuration.  If you've decreased the value of emstep,
>> there's little else that will account for such behavior.
>>
>> -Justin
>>
>> --
>> ========================================
>>
>> Justin A. Lemkul, Ph.D.
>> Research Scientist
>> Department of Biochemistry
>> Virginia Tech
>> Blacksburg, VA
>> jalemkul[at]vt.edu | (540) 231-9080
>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>
>> ========================================
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-- 
========================================

Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================