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

[Justin Lemkul]

On 3/4/13 4:11 PM, Miguel Ángel Mompeán García wrote:
> The version I was using this morning was 4.6
>

In that case, it's probably something worth pursuing.  Having the new version 
fail when an older version works is curious.  Can you please provide all of the 
following details:

1. Compilers used to build Gromacs
2. Hardware description
3. mdrun command
4. Complete .mdp file

-Justin

> 2013/3/4, Justin Lemkul <jalemkul at vt.edu>:
>>
>>
>> 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
>>
>> ========================================
>> --
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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

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