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

[Shima Arasteh]

The pressure convergence seems normal. I can not understand the reason of this fatal error.
I guess everything sounds normal, so what's the problem? Is it observable in my log file? Also potential , total energy are finite!


 Thanks Justin.

Sincerely,
Shima


----- Original Message -----
From: Justin Lemkul <jalemkul at vt.edu>
To: Shima Arasteh <shima_arasteh2001 at yahoo.com>; Discussion list for GROMACS users <gmx-users at gromacs.org>
Cc: 
Sent: Sunday, February 10, 2013 11:48 PM
Subject: Re: Fw: [gmx-users] Reg:1 particles communicated to PME node 0 are more than 2/3 times the cut-off



On 2/10/13 3:14 PM, Shima Arasteh wrote:
>   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?

An instantaneous value of pressure is meaningless.

http://www.gromacs.org/Documentation/Terminology/Pressure

> 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?
>

Well, for one, the system won't blow up ;)

The assessment of any equilibration is basically the same - do the observables 
of interest (temperature, pressure, etc) converge to the desired value?

-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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