From: Chris Harrison (charris5_at_gmail.com)
Date: Mon Jul 13 2009 - 09:54:50 CDT
Yogesh,
Two general, but not foolproof, approaches to resolving this problem
include:
1) increasing your cutoff and restarting (not "redo-ing") the simulation.
This is actually more of a "post-injury bandage" than cure for the
underlying issue that caused the problem and assumes whatever caused the
problem is over and will not continue or recur.
2) Decrease the output frequency of your dcd output to 10 or even 1 and redo
the simulation. When it crashes the output may dump some atom indices that
are exceeding velocities limits. Visualize the trajectory with VMD and
locate these atom's by creating a new rep (selection: serial "atom indices
from NAMD" ) using VDW. If no atom indices are dumped by NAMD, you will
still need to visualize the system with VMD to determine if your system is
exploding, imploding, has atoms or residues rapidly deviated from expected
behavior, etc.
Chris
-- Chris Harrison, Ph.D. Theoretical and Computational Biophysics Group NIH Resource for Macromolecular Modeling and Bioinformatics Beckman Institute for Advanced Science and Technology University of Illinois, 405 N. Mathews Ave., Urbana, IL 61801 char_at_ks.uiuc.edu Voice: 217-244-1733 http://www.ks.uiuc.edu/~char Fax: 217-244-6078 On Mon, Jul 13, 2009 at 5:57 AM, Yogesh Aher <aher.yogesh_at_gmail.com> wrote: > Dear NAMD- users! > > I was trying to run simple namd run for my homology-modelled protein which > is quite big in size. > It's PBC dimensions are like this (after solvating with option -t 5): > > # Periodic Boundary Conditions > cellBasisVector1 105. 0. 0. > cellBasisVector2 0. 121. 0. > cellBasisVector3 0. 0. 125. > cellOrigin 21. 73. 27. > PME GRID DIMENSIONS 108 128 128 > > But I get the following error: > Warning: Bad global exclusion count, possible error! > Warning: Increasing cutoff during minimization may avoid this. > > I increased cutoff values along with the pairlist-distance, but no impact > of them on avoiding this error. (Is there any rule of thumb to calculate > cutoff values depending on the PBC and PME dimensions?) > > I read other posts with the same subject, but couldn't get the relevant > solution, so thought to raise this question again. > > Looking forward for your valuable suggestions.. > > Thanking you, > Y. >
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