RE:Re: Help !!! ERROR: Atoms mooving too fast

From: Andrea Diaz (
Date: Tue Apr 03 2007 - 14:46:36 CDT


I have been running the equilibration again, minimizing for 5000 steps and increasing the pairlistdist parameter from 18.5 to 30 ( my cut off is 14 ), it didn't work. Now I am getting this error:

FATAL ERROR: Periodic cell has become too small for original patch grid!
Possible solutions are to restart from a recent checkpoint,
increase margin, or disable useFlexibleCell for liquid simulation.

I am giving the dimensions to the cell vectors using VMD, I used the minmax command and I assigned the value of the length of the box that I measure from vmd to the configuration file. Is this wrong ?

I am using NPT simulation, for that reason I don't believe that disable the UseFlexibleCell parameter was a good solution.

Thanks a lot .. I will be waiting for your suggestions


minimize for 2000 steps...I hope it will work!
The box seems too small..

Il giorno mer, 28/03/2007 alle 01.21 0200, Juan Diaz ha scritto:
> Hello everyone,
> I have a system of 3392 atoms of protein solvated in water, the total number of atoms is 5588. I am doing an equilibration of this system for 5ns using NPT ensamble at 300K and 1.013 Bar. The simulation have a problem and at 0.4ns it stops with this error:
> ERROR: Atom 3872 velocity is 22757.8 7703.94 155.571 (limit is 10000)
> ERROR: Atoms moving too fast; simulation has become unstable.
> ERROR: Exiting prematurely.
> I have attached the configuration file to this mail. I will be thankful if any person help me to solve this problem.
> Thanks,
> Andrea
> ¡Miles de amigos con tus mismas aficiones!
> ¡Miles de amigos con tus mismas aficiones!

Dr. Alessandro Casoni
Istituto di Chimica Organica "A. Marchesini"
Università degli Studi di Milano - Facoltà di Farmacia
Via G. Venezian 21, 20133 Milano
Tel.  390250314480 
FAX   390250314476
Miles de amigos con tus mismas aficiones!

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