From: Charles Danko (dankoc_at_gmail.com)
Date: Tue Nov 02 2004 - 11:20:21 CST
Hi,
Thanks to Brian for the help. I tried changing the interactions term
to scaled1-4 with the default scaling factor or 1.0 but the
minimization still died after 199 steps. The last couple steps are
pasted below. The energy is substantially different; I am not sure
that I understand the negative sign.
If there are any more suggestions I would be grateful.
Thanks again,
Charles
BRACKET: 2.50603e-07 0.090796 -114345 -267.772 826360
NEW SEARCH DIRECTION
INITIAL STEP: 6.4e-05
GRADIENT TOLERANCE: 14979.9
ENERGY: 195 14682.3820 22632.4249 7136.2497 282.3447
-96578.5816 9615.8599 0.0000 0.0000 0.0000
-42229.3205 0.0000 -42229.3205 -42229.3205 0.0000
ENERGY: 196 14352.5204 22506.1721 7126.8372 277.9901
-96822.7235 9098.0523 0.0000 0.0000 0.0000
-43461.1514 0.0000 -43461.1514 -43461.1514 0.0000
ENERGY: 197 14345.7336 22383.6335 7109.8393 271.1399
-97309.3368 8429.8700 0.0000 0.0000 0.0000
-44769.1205 0.0000 -44769.1205 -44769.1205 0.0000
ENERGY: 198 16752.9576 22839.6644 7095.3013 264.8575
-98275.7787 9208.5645 0.0000 0.0000 0.0000
-42114.4333 0.0000 -42114.4333 -42114.4333 0.0000
BRACKET: 0.000123859 2654.69 -4.84743e+07 -1.49018e+07 9.67884e+07
ENERGY: 199 14522.5983 22380.1473 7106.8166 269.4865
-97462.9771 8297.1243 0.0000 0.0000 0.0000
-44886.8042 0.0000 -44886.8042 -44886.8042 0.0000
LDB: LOAD: AVG 121.372 MAX 150.69 MSGS: TOTAL 171 MAXC 36 MAXP 4 None
LDB: LOAD: AVG 121.372 MAX 145.646 MSGS: TOTAL 310 MAXC 88 MAXP 4 Alg7
LDB: LOAD: AVG 121.372 MAX 123.798 MSGS: TOTAL 310 MAXC 88 MAXP 4 Alg7
Rtasks fail:
Rtask(s) 1 : exited with signal <11>
Rtask(s) 4 2 3 7 5 6 8 10 9 : exited with signal <15>
Rtask(s) 1 : coredump
On Mon, 1 Nov 2004 15:56:32 -0800 (PST), Brian Bennion
<brian_at_youkai.llnl.gov> wrote:
> 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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