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

[Miguel Ángel Mompeán García]

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?


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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