AMBER Archive (2004)

Subject: RE: AMBER: SHAKE probelm

From: Huang, Hai (hai.huang_at_vanderbilt.edu)
Date: Fri Nov 19 2004 - 16:56:54 CST

Hi, Ross,

Thank you for your helpful suggestions, I run 1,000 frames as you adviced and viewed the result with VMD. It seems that the system is unstable, so which reason may cause the unstability? Actually, before running MD, I have carried out a short time minimization. BTW, I checked my starting structure again, I didn't find any atoms too close.

Hai

-----Original Message-----
From: owner-amber_at_scripps.edu on behalf of Ross Walker
Sent: Fri 11/19/2004 11:35 AM
To: amber_at_scripps.edu
Subject: RE: AMBER: SHAKE probelm
 
Your system is probably unstable. With shake off have you looked carefully
at the structure over time (mdcrd)? What about the energies and the
temperature?
 
Try running 1,000 frames or so with ntwx set to 1. Then visualise it in
something like VMD, the problem should be obvious, you either have two atoms
close together or your system is unstable. I trust you have carried out
extensive minimisation on your system before starting MD.
 
All the best
Ross

  _____

From: owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu] On Behalf Of
Huang, Hai
Sent: 19 November 2004 08:25
To: amber_at_scripps.edu
Subject: AMBER: SHAKE probelm

Hi, all,

I am a new user of AMBER. I generated a crosslink of oligonucleotide and
peptide with amber7. I try to simulate its structrure with molecular
dynamics, it works well with SHAKE off (ntc=1, ntf=1), however, when SHAKE
is turned on (ntc=2, ntf=2), the running crashs rapidly and error message
appears:
     Coordinate resetting (SHAKE) cannot be accomplished,
     deviation is too large
     NITER, NIT, LL, I and J are : 0 11 7 12 13

     Note: This is usually a symptom of some deeper
     problem with the energetics of the system.

I have carefully checked the structure. LEAP doesn't report any error or
warning. Does anyone have any idea about this problem? Thank you.

Hai Huang

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