[gmx-users] X particles communicated to PME node Y are more ...
Miguel Ángel Mompeán García
mig.mompean at gmail.com
Thu Mar 7 19:17:27 CET 2013
2013/3/4 Justin Lemkul <jalemkul at vt.edu>
> Dear Justin,
>
With 4.5.5 the jobs have completed. I am going to repeat them with 4.6.1
If you find something weird in the mdp file or require further explanations
on the points do mention I will do my best to provide the necessary info.
Right below are the comments:
> 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
These lines are from the CMakeOutput.log file:
The system is: Linux - 2.6.32-5-amd64 - x86_64 (*****)
Compiling the C compiler identification source file "CMakeCCompilerId.c"
succeeded.
Compiler: /usr/bin/gcc
cc -v: gcc version 4.4.5
3. mdrun command
> 4. Complete .mdp file
grompp -f minimize.mdp -c Mut3.gro -o em.tpr -p topol.top
mdrun -v -deffnm em
The minimize.mdp file:
integrator = steep
emtol = 1000.0
emstep = 0.01
nsteps = 50000
nstlist = 1
ns_type = grid
rlist = 1.0
coulombtype = PME
rcoulomb = 1.0
rvdw = 1.0
pbc = xyz
Thank-you a lot for all your tips and comments,
Miguel
>
>
> -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<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>>>>>
>>>>> ==============================**==========
>>>>> --
>>>>> gmx-users mailing list gmx-users at gromacs.org
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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<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>>>
>>> ==============================**==========
>>> --
>>> gmx-users mailing list gmx-users at gromacs.org
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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<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>
> ==============================**==========
> --
> gmx-users mailing list gmx-users at gromacs.org
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