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

[Shima Arasteh]

 Hi,

I get the same error, but the information written in my log file is as :

   Energies (kJ/mol)
            U-B    Proper Dih.  Improper Dih.      CMAP Dih.          LJ-14
    8.26180e+04    5.53024e+04    6.50084e+02   -2.83474e+02    8.50267e+03
     Coulomb-14        LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip.
   -1.06730e+05    7.84233e+04   -7.99529e+03   -9.89064e+05   -2.54063e+04
      Potential    Kinetic En.   Total Energy    Temperature Pres. DC (bar)
   -9.03982e+05    3.53794e+05   -5.50188e+05    4.26000e+02   -1.34125e+02
 Pressure (bar)   Constr. rmsd
   -1.97048e+04    5.76582e-04

The temperature is around 400, it seems normal, but the pressure is negative! Is it the problem which causes my system get this fatal error?
I changed the pressure coupling to Berendsen and decrease the time step to 1fs. How would I be sure that my modifications is beneficial? By checking the pressure in log file passing the time?


I would be appreciate you to help me. 
Thanks in advance.

Sincerely,
Shima

----- Forwarded Message -----
From: Shima Arasteh <shima_arasteh2001 at yahoo.com>
To: Discussion list for GROMACS users <gmx-users at gromacs.org> 
Sent: Friday, February 8, 2013 5:42 PM
Subject: Re: [gmx-users] Reg:1 particles communicated to PME node 0 are more than 2/3 times the cut-off



Doesn't that mean the npt should be done for a longer time?


Sincerely,
Shima


________________________________
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
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