[gmx-users] unstable system

[Justin Lemkul]

On 5/7/13 2:42 PM, Shima Arasteh wrote:
> Hi,
>
> 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.
>

There is no reason why NPT should run stably but MD would then fail.  The high 
initial temperature suggests that atoms are overlapping somehow or that the 
previous state has not been preserved properly.  Please provide exact details of 
what you are doing, including the following:

1. Exact commands given in the preparation protocol (EM and equilibration)
2. The .mdp files being used for all steps, most importantly NPT and MD
3. Your grompp and mdrun invocations for the failing MD run

-Justin

> ----- 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: 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
>
> --
> ========================================
>
> 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
>
> ========================================

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

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

========================================