From: Brian Bennion (brian_at_youkai.llnl.gov)
Date: Mon Nov 01 2004 - 17:56:32 CST
HI Charles,
Is there a particular reason you use a 1-2 exclusion instead of a 1-4
exclusion?
your vdw energies are not at all good and I think it is because your
including too many interactions with the 1-2 based exclusion.
Just for kicks, try using the 1-4 term and see how things go.
Regards
Brian
On Mon, 1 Nov 2004, Charles Danko wrote:
> 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
>
*****************************************************************
**Brian Bennion, Ph.D. **
**Computational and Systems Biology Division **
**Biology and Biotechnology Research Program **
**Lawrence Livermore National Laboratory **
**P.O. Box 808, L-448 bennion1_at_llnl.gov **
**7000 East Avenue phone: (925) 422-5722 **
**Livermore, CA 94550 fax: (925) 424-6605 **
*****************************************************************
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