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

From: Luis Cunha (Luis.Cunha_at_mssm.edu)
Date: Tue Apr 03 2007 - 20:53:10 CDT

Hi Andrea,
I've run into that problem a few times. I found that the solution sugested here http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l/2067.html
solved the problem. Usually after restarting the simulation 2 or 3 times, the problem goes way.

Luis Cunha
Dept of Genetic and Genomic Sciences
Mount Sinai School of Medicine of the New York university
New York, NY

----- Original Message -----
From: Andrea Diaz <jd2006_at_latinmail.com>
Date: Tuesday, April 3, 2007 4:15 pm
Subject: RE:Re: namd-l: Help !!! ERROR: Atoms mooving too fast
To: "namd-l_at_ks.uiuc.edu" <namd-l_at_ks.uiuc.edu>, "alessandro.casoni_at_studenti.unimi.it" <alessandro.casoni_at_studenti.unimi.it>
Cc: "namd-l_at_ks.uiuc.edu" <namd-l_at_ks.uiuc.edu>

> Hello,
>
> 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
>
> Andrea
>
> minimize for 2000 steps...I hope it will work!
> The box seems too small..
>
> Alessandro
> 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! http://www.latinchat.com
> >
> > ¡Miles de amigos con tus mismas aficiones! http://www.latinchat.com
> --
> Dr. Alessandro Casoni
> Istituto di Chimica Organica "A. Marchesini"
> Università degli Studi di Milano - Facoltà di Farmacia
> Via G. Venezian 21, 20133 Milano
> E-Mail: alessandro.casoni_at_unimi.it
> Tel. 390250314480
> FAX 390250314476
>
>
>
> Miles de amigos con tus mismas aficiones! http://www.latinchat.com

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