[gmx-users] Reg:1 particles communicated to PME node 0 are more than 2/3 times the cut-off

[Justin Lemkul]

On 2/8/13 9:12 AM, Shima Arasteh wrote:
>
>
> Doesn't that mean the npt should be done for a longer time?
>

No.  Look at the snippet of the .log file - the temperature at step zero is > 
1800K!  That indicates that the system is wildly unstable from the very start. 
Solutions to the problem are suggested in the link Mark provided, which have 
also been posted thousands of times to this list ;)

-Justin

> From: Mark Abraham <mark.j.abraham at gmail.com>
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Sent: Friday, February 8, 2013 5:37 PM
> Subject: Re: [gmx-users] Reg:1 particles communicated to PME node 0 are more than 2/3 times the cut-off
>
> On Fri, Feb 8, 2013 at 7:48 AM, Subramaniam Boopathi
> <boopathiphd at gmail.com>wrote:
>
>> dear sir,
>>              how can i remove this following problem
>>
>
>
>>      Energies (kJ/mol)
>>             Angle    Proper Dih.  Improper Dih.          LJ-14     Coulomb-14
>>       2.36059e+03    3.53976e+02    7.34586e+00    7.00084e+03    2.02621e+03
>>           LJ (SR)   Coulomb (SR)   Coul. recip. Position Rest.      Potential
>>       7.70414e+03   -5.91044e+04   -6.76092e+03    1.80260e+00   -4.64104e+04
>>       Kinetic En.   Total Energy  Conserved En.    Temperature Pressure (bar)
>>       6.48550e+04    1.84446e+04    1.84446e+04    1.88479e+03    7.32453e+03
>>      Constr. rmsd
>>       4.81184e-01
>>
>>
>> -------------------------------------------------------
>> Program mdrun_d, VERSION 4.5.5
>> Source code file: pme.c, line: 538
>>
>> Fatal error:
>> 1 particles communicated to PME node 0 are more than 2/3 times the cut-off
>> out of the domain decomposition cell of their charge group in dimension y.
>> This usually means that your system is not well equilibrated.
>> For more information and tips for troubleshooting, please check the GROMACS
>> website at http://www.gromacs.org/Documentation/Errors
>> -------------------------------------------------------
>>
>
> Did you try following the link mdrun suggested? :-)
>
> Mark
>

-- 
========================================

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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