From: David Tanner (guacamoleo_at_gmail.com)
Date: Mon Apr 04 2011 - 16:34:11 CDT
The below output is normal for systems with atoms which are initially
very close together such that their repulsive forces are very large.
Try minimizing this same system in vacuum (no explicit water and GBIS
turned off) to verify that your problem is not with implicit solvent
but rather a problem with the system's initial coordinates.
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
David E. Tanner
Theoretical and Computational Biophysics Group
3159 Beckman Institute
University of Illinois at Urbana-Champaign
405 N. Mathews
Urbana, IL 61801
http://www.linkedin.com/in/davidetanner
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On Apr 4, 2011, at 3:47 PM, harish vashisth wrote:
Dear all,
I am sorry if anyone is getting this email twice. I have been
trying to use new implicit solvent feature in recently released
NAMDv2.8b1 (64 bit Linux_X86_64 binary and ran using ++local option).
I tried default options suggested in NAMD user's guide (http://www.ks.uiuc.edu/Research/namd/2.8b1/ug/node31.html
), and have tried both with and without PBCs, but I start getting some
weird output right at the beginning of these runs. No dcd files are
updated after two or three frames. The kind of output I get during
initial minimization steps looks like as given below.
The input files for this run can be downloaded from the following link:
http://sitemaker.umich.edu/harish.vashisth/home
Any help would be great. Thank you so much.
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========================================================================
MINIMIZER SLOWLY MOVING 1 ATOMS WITH BAD CONTACTS DOWNHILL
PRESSURE: 27 2198.64 98.2676 21.3003 98.2676 2114.29 -160.482 21.3003
-160.482 2326.12
GPRESSURE: 27 nan nan nan nan nan nan nan nan nan
ENERGY: 27 142506.0681 34522.7769 1025.3743
51.7267 -958225.7788 9999999999.9999 0.0000
0.0000 0.0000 9999999999.9999 0.0000
9999999999.9999 9999999999.9999 0.0000 2213.0139
9999999999.9999 555899.7610 2213.0139 9999999999.9999
MINIMIZER SLOWLY MOVING 1 ATOMS WITH BAD CONTACTS DOWNHILL
PRESSURE: 28 2198.99 97.9171 21.2457 97.9171 2116.46 -161.112 21.2457
-161.112 2326.4
GPRESSURE: 28 nan nan nan nan nan nan nan nan nan
ENERGY: 28 142507.7791 34521.3553 1024.9075
50.3971 -958456.7341 9999999999.9999 0.0000
0.0000 0.0000 9999999999.9999 0.0000
9999999999.9999 9999999999.9999 0.0000 2213.9492
9999999999.9999 555899.7610 2213.9492 9999999999.9999
MINIMIZER STARTING CONJUGATE GRADIENT ALGORITHM
LINE MINIMIZER REDUCING GRADIENT FROM nan TO nan
LINE MINIMIZER BRACKET: DX 0 0 DU 0 0 DUDX nan nan nan
MINIMIZER RESTARTING CONJUGATE GRADIENT ALGORITHM
LINE MINIMIZER REDUCING GRADIENT FROM nan TO nan
LINE MINIMIZER BRACKET: DX 0 0 DU 0 0 DUDX nan nan nan
MINIMIZER RESTARTING CONJUGATE GRADIENT ALGORITHM
LINE MINIMIZER REDUCING GRADIENT FROM nan TO nan
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========================================================================
Regards,
-Harish Vashisth
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