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

[Justin Lemkul]

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

-- 
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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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