Dear all,
I have a problem with the cutoff of the energy gradient (drms) during
a constrained optimization using sander (the problem persist with
version 10 or 11,
and on three different computers).
I struggled a lot before writing, because the problem is apparently so stupid
that I thought I missed something, but I am unable to find out what.
Essentially I want to perform a tough optimization to perform nm analysis,
so I put a drms value of 10-10 in the input.
No matter which algorithm I use, the program exits without errors at 10-7 in
the value of rms, which does not guarantee to have all positive frequencies
in nm calculations.
I don't know what I am doing wrong or if the problem is the definition of drms.
I read in the posts that nab should allow reach very low values of forces, but
I would like to avoid its usage since I have everything (many scripts included!)
to run with sander and nmode.
I report the input and the output of the calculations. The system has
~3500 atoms
and its extension is ~50 A.
Thanks in advance!
Attilio
INPUT
File generated by mm_pbsa.pl
&cntrl
ntxo = 1,
ntf = 1, ntb = 0, ibelly=1
dielc = 1,
cut = 99.0, nsnb = 99999,
scnb = 2.0, scee = 1.2,
imin = 1, ntmin=3, maxcyc = 100000,
ncyc = 0, drms = 0.0000000001
&end
--Belly
ATOM 88 108
ATOM 171 223
ATOM 271 284
ATOM 374 384
ATOM 401 415
ATOM 449 569
ATOM 790 896
ATOM 959 1083
ATOM 1132 1226
ATOM 1302 1362
ATOM 1391 1410
ATOM 1513 1565
ATOM 1679 1792
ATOM 1803 1833
ATOM 1872 1927
ATOM 1971 1990
ATOM 2005 2066
ATOM 2098 2119
ATOM 2230 2248
ATOM 2292 2370
ATOM 2377 2382
ATOM 2392 2400
ATOM 2410 2418
ATOM 2422 2427
ATOM 2431 2436
ATOM 2452 2457
ATOM 2461 2472
ATOM 2476 2478
ATOM 2482 2487
ATOM 2497 2499
ATOM 2503 2517
ATOM 2521 2523
ATOM 2539 2544
ATOM 2548 2556
ATOM 2563 2568
ATOM 2572 2577
ATOM 2590 2592
ATOM 2596 2598
ATOM 2602 2613
ATOM 2617 2619
ATOM 2623 2628
ATOM 2641 2643
ATOM 2659 2667
ATOM 2671 2673
ATOM 2677 2679
ATOM 2683 2688
ATOM 2692 2706
ATOM 2713 2724
ATOM 2731 2736
ATOM 2743 2745
ATOM 2749 2751
ATOM 2755 2760
ATOM 2776 2781
ATOM 2785 2802
ATOM 2818 2823
ATOM 2833 2835
ATOM 2872 2877
ATOM 2884 2895
ATOM 2902 2904
ATOM 2908 2913
ATOM 2917 2919
ATOM 2926 2928
ATOM 2932 2934
ATOM 2944 2946
ATOM 2956 2961
ATOM 2965 2967
ATOM 2974 2976
ATOM 2983 2994
ATOM 2998 3003
ATOM 3007 3009
END
END
OUTPUT
-------------------------------------------------------
Amber 11 SANDER 2010
-------------------------------------------------------
| Run on 12/03/2011 at 22:38:29
[-O]verwriting output
File Assignments:
| MDIN: sanmin_com.in
| MDOUT: sanmin_com.1.out
|INPCRD: ./1_tr_wat_com.crd.1
| PARM: compl_wat_tr_1.parm7
|RESTRT: sanmin_com.1.restrt
| REFC: refc
| MDVEL: mdvel
| MDEN: mden
| MDCRD: mdcrd
|MDINFO: mdinfo
| MTMD: mtmd
|INPDIP: inpdip
|RSTDIP: rstdip
|INPTRA: inptraj
|
Here is the input file:
File generated by mm_pbsa.pl
&cntrl
ntxo = 1,
ntf = 1, ntb = 0, ibelly=1
dielc = 1,
cut = 99.0, nsnb = 99999,
scnb = 2.0, scee = 1.2,
imin = 1, ntmin=3, maxcyc = 100000,
ncyc = 0, drms = 0.0000000001
&end
--Belly
ATOM 88 108
ATOM 171 223
ATOM 271 284
ATOM 374 384
ATOM 401 415
ATOM 449 569
ATOM 790 896
ATOM 959 1083
ATOM 1132 1226
ATOM 1302 1362
ATOM 1391 1410
ATOM 1513 1565
ATOM 1679 1792
ATOM 1803 1833
ATOM 1872 1927
ATOM 1971 1990
ATOM 2005 2066
ATOM 2098 2119
ATOM 2230 2248
ATOM 2292 2370
ATOM 2377 2382
ATOM 2392 2400
ATOM 2410 2418
ATOM 2422 2427
ATOM 2431 2436
ATOM 2452 2457
ATOM 2461 2472
ATOM 2476 2478
ATOM 2482 2487
ATOM 2497 2499
ATOM 2503 2517
ATOM 2521 2523
ATOM 2539 2544
ATOM 2548 2556
ATOM 2563 2568
ATOM 2572 2577
ATOM 2590 2592
ATOM 2596 2598
ATOM 2602 2613
ATOM 2617 2619
ATOM 2623 2628
ATOM 2641 2643
ATOM 2659 2667
ATOM 2671 2673
ATOM 2677 2679
ATOM 2683 2688
ATOM 2692 2706
ATOM 2713 2724
ATOM 2731 2736
ATOM 2743 2745
ATOM 2749 2751
ATOM 2755 2760
ATOM 2776 2781
ATOM 2785 2802
ATOM 2818 2823
ATOM 2833 2835
ATOM 2872 2877
ATOM 2884 2895
ATOM 2902 2904
ATOM 2908 2913
ATOM 2917 2919
ATOM 2926 2928
ATOM 2932 2934
ATOM 2944 2946
ATOM 2956 2961
ATOM 2965 2967
ATOM 2974 2976
ATOM 2983 2994
ATOM 2998 3003
ATOM 3007 3009
END
END
--------------------------------------------------------------------------------
1. RESOURCE USE:
--------------------------------------------------------------------------------
| Flags:
| NONPERIODIC ntb=0 and igb=0: Setting up nonperiodic simulation
| *** cutoff > system size, list only builds once
|Largest sphere to fit in unit cell has radius = 49.394
| New format PARM file being parsed.
| Version = 1.000 Date = 12/03/11 Time = 22:11:59
NATOM = 3008 NTYPES = 14 NBONH = 1829 MBONA = 1173
NTHETH = 2669 MTHETA = 1550 NPHIH = 5128 MPHIA = 3688
NHPARM = 0 NPARM = 0 NNB = 13533 NRES = 365
NBONA = 1173 NTHETA = 1550 NPHIA = 3688 NUMBND = 46
NUMANG = 92 NPTRA = 65 NATYP = 32 NPHB = 1
IFBOX = 0 NMXRS = 79 IFCAP = 0 NEXTRA = 0
NCOPY = 0
....
....
NSTEP ENERGY RMS GMAX NAME NUMBER
1749 -1.1626E+04 1.6283E-05 4.7472E-04 C23 2356
BOND = 139.6422 ANGLE = 133.7998 DIHED = 717.5460
VDWAALS = -651.1000 EEL = -16266.5476 HBOND = 0.0000
1-4 VDW = 256.4588 1-4 EEL = 4043.8941 RESTRAINT = 0.0000
NSTEP ENERGY RMS GMAX NAME NUMBER
1799 -1.1626E+04 9.3553E-06 1.5970E-04 CD 411
BOND = 139.6421 ANGLE = 133.7997 DIHED = 717.5459
VDWAALS = -651.1001 EEL = -16266.5477 HBOND = 0.0000
1-4 VDW = 256.4589 1-4 EEL = 4043.8944 RESTRAINT = 0.0000
--------------------------------------------------------------------------------
5. TIMINGS
--------------------------------------------------------------------------------
| Build the list 0.26 (98.77% of List )
| Other 0.00 ( 1.23% of List )
| List time 0.26 ( 0.04% of Nonbo)
| Short_ene time 647.65 (100.0% of Direc)
| Other 0.28 ( 0.04% of Direc)
| Direct Ewald time 647.93 (99.89% of Ewald)
| Other 0.69 ( 0.11% of Ewald)
| Ewald time 648.63 (100.0% of Nonbo)
| Nonbond force 648.89 (98.87% of Force)
| Bond/Angle/Dihedral 7.38 ( 1.12% of Force)
| Other 0.06 ( 0.01% of Force)
| Force time 656.33 (100.0% of Runmd)
| Runmd Time 656.33 (99.31% of Total)
| Other 4.54 ( 0.69% of Total)
| Total time 660.88 (100.0% of ALL )
| Highest rstack allocated: 14660
| Highest istack allocated: 2932
| Job began at 22:38:29.143 on 12/03/2011
| Setup done at 22:38:29.332 on 12/03/2011
| Run done at 22:49:30.027 on 12/03/2011
| wallclock() was called 60915 times
--
¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤
Attilio Vittorio Vargiu, PhD
SLACS & Department of Physics, University of Cagliari
Cittadella Universitaria S.P. Monserrato-Sestu Km 0.700
09042 Monserrato (CA), Italy
e-mail1: vargiu.dsf.unica.it
e-mail2: attilio.vargiu.gmail.com
Phone: +390706754847
Fax: +39070510171
¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤
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Received on Sun Dec 04 2011 - 00:00:02 PST
