From: Charles Danko (dankoc_at_gmail.com)
Date: Mon Nov 01 2004 - 16:30:12 CST
Hi,
I am having a problem minimizing my system. The end of the
minimization output file is as follows:
ENERGY: 196 72896.2480 36970.3755 7529.1929 527.0135
302178.7322 230719.2954 0.0000 0.0000 0.0000
650820.8576 0.0000 650820.8576 650820.8576 0.0000
ENERGY: 197 74621.1928 37566.9383 7549.9188 527.7283
301273.8956 231103.4061 0.0000 0.0000 0.0000
652643.0800 0.0000 652643.0800 652643.0800 0.0000
BRACKET: 0.000110482 1822.22 -4.75282e+07 -1.29993e+07 6.80802e+07
ENERGY: 198 73119.1726 37051.1602 7532.4822 526.9988
302022.8627 230476.5677 0.0000 0.0000 0.0000
650729.2442 0.0000 650729.2442 650729.2442 0.0000
BRACKET: 7.36549e-05 1913.84 -1.29993e+07 -1.34062e+06 6.80802e+07
ENERGY: 199 73237.2018 37093.2432 7534.1100 527.0121
301947.9529 230399.3378 0.0000 0.0000 0.0000
650738.8579 0.0000 650738.8579 650738.8579 0.0000
LDB: LOAD: AVG 163.034 MAX 257.747 MSGS: TOTAL 240 MAXC 44 MAXP 4 None
LDB: LOAD: AVG 163.034 MAX 195.64 MSGS: TOTAL 526 MAXC 145 MAXP 6 Alg7
LDB: LOAD: AVG 163.034 MAX 166.29 MSGS: TOTAL 530 MAXC 145 MAXP 6 Alg7
Rtasks fail:
Rtask(s) 1 : exited with signal <11>
Rtask(s) 2 5 4 3 9 6 8 7 10 : exited with signal <15>
Rtask(s) 1 : coredump
>
I am using the script which is pasted below. So far, I have tried:
decreasing the parameters minBabyStep and minTinyStep by 1, 2, and 3
orders of magnitude; running minimization with the velocity quenching
algorithm, and starting from a restart file. In all cases the system
craps out after exactly 199 steps, including when the system is
started from the restart file.
My input files are rather large (~5MB pdb, ~10MB psf) but I can post
if someone requests.
I think that I am most likely missing something obvious.
Thanks in advance for any help,
Charles
# initial config
coordinates ../final.pdb
structure ../final.psf
temperature 0
# output params
outputtiming 1000
outputname ./output/minimize
binaryoutput no
# for restart
restartname ./minimize/system_minimize_restart
restartfreq 100
restartsave yes
binaryrestart yes; # preserves more accuracy.
# integrator params
timestep 1.0
# force field params
paratypecharmm on
parameters par_all27_prot_lipid.prm
exclude 1-2
switching on
switchdist 8.0
cutoff 12.0
pairlistdist 13.5
stepspercycle 20
#velocityQuenching on
#minimizethe yffstem
minimization on; #this turns on fast minimization
minTinyStep 1.0e-7;
#minbabystep 1.0e-3; #If it doesnt work, this option is on for the next run.
minimize 2000
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