[gmx-users] unstable system

Shima Arasteh shima_arasteh2001 at yahoo.com
Tue May 7 20:42:47 CEST 2013


I have run a new npt after energy minimization on my system composed of water/protein/lipid/ions. 
After a few nanoseconds for NPT, I ran MD, and got fatal error :

X particles communicated to PME node Y are more than a cell length out of the domain decomposition cell of their charge group

What is written in md.log file shows an improper pressure,
           Step           Time         Lambda
              0        0.00000        0.00000

   Energies (kJ/mol)
            U-B    Proper Dih.  Improper Dih.      CMAP Dih.          LJ-14
    8.26284e+04    5.54129e+04    7.43891e+02   -1.96405e+02    8.37087e+03
     Coulomb-14        LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip.
   -1.05973e+05    8.51736e+04   -5.79669e+03   -1.11865e+06   -2.67464e+05
 Position Rest.      Potential    Kinetic En.   Total Energy    Temperature
    2.09408e+03   -1.26366e+06    3.33724e+05   -9.29932e+05    4.44648e+02
 Pres. DC (bar) Pressure (bar)   Constr. rmsd
   -1.09245e+02   -2.40668e+04    6.65938e-04

I' d like to know if it means that more that the system is required of more npt equilibration? 

Thanks for your suggestion. Please help me.


----- 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>
Sent: Friday, April 19, 2013 11:29 PM
Subject: Re: [gmx-users] unstable system

On 4/19/13 2:57 PM, Shima Arasteh wrote:
> Thanks so much for your replies. I appreciate you.
> Do you think that more NPT equilibration might solve the problem? or wont work?

I have no idea at what point you are in your procedure that is crashing.  I'm 
not going to make some blind assessment of "do more NPT" or some random thing. 
If you just completed the EM as you posted, proceed with whatever equilibration 
protocol you believe to be sufficient.  There is no one single answer here.  If 
you're jumping straight into MD after the EM you showed, you need to start your 
equilibration over again completely.



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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