Re: vmd-l: Interactive Simulations, ligand size limits....

From: Luis Rosales (
Date: Wed Apr 20 2005 - 18:19:58 CDT

 Hi John,

I have 2 proteins of about 80 residues each without explicit water, so I
think that the system is small-medium size...

About the crash, it happpens when I touch the molecule with the "mouse >
apply force > fragment" activated. In the best cases, I could see tiny
arrowheads appearing before the simulation dies. However I dont have
problems rotating, scaling, translating the system during the simulation.
I could apply force to individual atoms and residues without any problems,
as long as the force is not too big, as you said.
So, the problem happens when I intend to apply a force on a molecule bigger
than 15 residues.

I must apologize, just realized that I did not saved the error message, but
I will reproduce the problem and send to you the message as soon I got it...

Thanks for your help,


Open WebMail Project (
---------- Original Message -----------
From: John Stone <>
To: Luis Rosales <>
Sent: Wed, 20 Apr 2005 16:12:20 -0500
Subject: Re: vmd-l: Interactive Simulations, ligand size limits....
> Luis,
>   How large is the molecule you're simulating?  When you say that
> the simulation "crashed", does that mean that NAMD aborted because
> you pulled too hard (margin violation, exceeding the speed of light, 
> etc...), or did NAMD actually have a seg fault or floating point exception
> of some kind?   If you got a "margin violation" it means that you pulled
> on the structure so hard that you exceeded NAMD's internal limit on
> atom velocity imposed by the spatial decomposition it uses.  If you
> pull to hard and impart a tremendous velocity per simulated timestep,
>  this means that either you need to pull more gently, or you need to 
> decrease the gap in timescale between your real-time pulling and the 
> rate of simulated time in the simulation, either by using a smaller 
> molecule or by using fixed atoms, or some combination of both.
>   John Stone
> -- 
> NIH Resource for Macromolecular Modeling and Bioinformatics
> Beckman Institute for Advanced Science and Technology
> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> Email:                 Phone: 217-244-3349         
>        WWW:      Fax: 217-244-6078
------- End of Original Message -------

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