[AMBER] problem setting drms to low values

From: Attilio Vittorio Vargiu <attilio.vargiu.gmail.com>
Date: Sat, 3 Dec 2011 23:31:53 -0800

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

-- 
いいいいいいいいいいいいいいいいいいいいいいいいいいいいい
         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
いいいいいいいいいいいいいいいいいいいいいいいいいいいいい
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Received on Sun Dec 04 2011 - 00:00:02 PST
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