bugAdun - Bugs: bug #9283, Charmm minimisation and dynamic...

 
 
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bug #9283: Charmm minimisation and dynamic (analysis)

Submitted by:  Gian Pietro Miscione <giampi>
Submitted on:  Wed 06 Jun 2007 09:45:42 AM UTC  
 
Category: NoneSeverity: 3 - Normal
Priority: 1 - LaterStatus: None
Privacy: PublicAssigned to: None
Open/Closed: OpenRelease: None
Operating System: NonePlanned Release: None

Wed 21 Apr 2010 06:17:23 PM UTC, comment #1:

was this solved?

Jordi VillĂ -Freixa <jvilla>
Project Administrator
Wed 06 Jun 2007 09:45:42 AM UTC, original submission:

I am trying to study a system (TIM aka TPI) consisting of 7536 atoms and 494 residues with charmm in gas phase.

When building the system, I have the following problems:
1) a lot of FourierTorsion interactions are missing
2) a lot of HarmonicImproperTorsion interactions are missing
3) patching residues can't be treated/added properly

I then try to run an initial minimisation:
the calculation proceeds well (I visualized it with VMD while running) until the simulation fails after a few steps.
When I try to upload it for an analysis, the application crahes.

If I try to run a dynamic calculation, the simulation proceeds well (I visualized it with VMD while running) until some atoms begin to get very close to each other and pushed away -> the calculation fails.
When I try to upload it for an analysis, the application crahes.

Attaching both the system and the template.

G.

Gian Pietro Miscione <giampi>

 

Attached Files
file #2404:  TIM_system.tar.gz added by giampi (372kB - application/x-gzip)
file #2403:  template_Gassystem added by giampi (40kB - application/octet-stream)

 

Depends on the following items: None found

Items that depend on this one: None found

 

Carbon-Copy List
  • -unavailable- added by jvilla (Posted a comment)
  • -unavailable- added by giampi (Submitted the item)
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    Follow 2 latest changes.

    Date Changed By Updated Field Previous Value => Replaced By
    Wed 06 Jun 2007 09:55:01 AM UTCgiampiAttached File-=>Added TIM_system.tar.gz, #2404
    Wed 06 Jun 2007 09:45:42 AM UTCgiampiAttached File-=>Added template_Gassystem, #2403
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