[gmx-users] Fwd: mdrun error

[Justin A. Lemkul]

Amir Marcovitz wrote:
> 
> 
> ---------- Forwarded message ----------
> From: *Amir Marcovitz* <amarcovitz at gmail.com <mailto:amarcovitz at gmail.com>>
> Date: Mon, Jan 4, 2010 at 6:18 PM
> Subject: mdrun error
> To: gmx-users-request at gromacs.org <mailto:gmx-users-request at gromacs.org>
> 
> 
> Hi,
>  
> my system is composed of 2 molecules that are arranged in a lattice: 
> i.e., each molecule is represented by 4 atoms (which are charged) and 
> organized in a square lattice.
>  
> bonds, angles and dihedrals connect the 4 atoms on each lattice.
>  
> i want to simulate the 2 'plates' such that they are parallel so i added 
> 90 degrees, inter-lattice angles between selected atoms in the system to 
> the [angles] section in the *.top file
> the processing with grompp worked fine but the mdrun aborted with the 
> following error:
>  
> *-------------------------------------------------------
> Program mdrun, VERSION 4.0.5
> Source code file: nsgrid.c, line: 348*
> *Fatal error:
> Number of grid cells is zero. Probably the system and box collapsed.*
> *-------------------------------------------------------
> * 
> beforehand the following massages poped-up:
>  
> * t = 2.954 ps: Water molecule starting at atom 9891 can not be settled.
> Check for bad contacts and/or reduce the timestep.
> Wrote pdb files with previous and current coordinates*
> ** 
> and* *
> ** 
> *Step 1478  Warning: pressure scaling more than 1%, mu: 1.95218 1.95218 
> 1.95218*
> ** 
> does anyone has a clue of what is wrong?

All of these messages indicate that your system has become unstable, for which 
there could be a number of reasons (insufficient minimization/equilibration, 
lousy parameters, inappropriate .mdp settings, etc).  For more detailed advice, 
consult the wiki:

http://www.gromacs.org/Documentation/Errors#Pressure_scaling_more_than_1.25
http://www.gromacs.org/Documentation/Errors#LINCS.2fSETTLE.2fSHAKE_warnings
http://www.gromacs.org/Documentation/Terminology/Blowing_Up

If you need further help, post the procedure you have used to prepare the 
system, the outcome of energy minimization, and your .mdp file.

-Justin

> Thanks, Amir
> 
> 
>  
> 

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

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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