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

Miguel Ángel Mompeán García mig.mompean at gmail.com
Mon Mar 4 22:11:55 CET 2013


The version I was using this morning was 4.6

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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