From: Luis Rosales (ludwig_at_correo.biomedicas.unam.mx)
Date: Wed Apr 20 2005 - 18:19:58 CDT
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 (http://openwebmail.org) ---------- Original Message ----------- From: John Stone <johns_at_ks.uiuc.edu> To: Luis Rosales <ludwig_at_correo.biomedicas.unam.mx> Cc: namd-l_at_ks.uiuc.edu, vmd-l_at_ks.uiuc.edu 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 > vmd_at_ks.uiuc.edu > > -- > 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: johns_at_ks.uiuc.edu Phone: 217-244-3349 > WWW: http://www.ks.uiuc.edu/~johns/ Fax: 217-244-6078 ------- End of Original Message -------
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