AMBER Archive (2002)

Subject: Problem with Gibbs 2D run

From: Asif Rahaman (arahaman_at_chemdept.chem.ou.edu)
Date: Sun Jun 02 2002 - 22:29:38 CDT

Dear All:

     I am trying to make a 2D run using Gibbs. The following is my input file.

----------------------------
  QBN, HP,QAA,AIJ,isodown, PMF to rotate Glh L212
  &cntrl irest=0, ibelly=1,
   ntx=1, ntxo=1, ig=150899, tempi=300.0,
   ntb=0,
   nrun=1681, ntt=1, temp0=300.0, dtemp=00.0, tautp=0.2,
   ndfmin = 0, ntcm = 1, nscm = 0,
   nstlim = 10, init = 3, t=0.0, dt=0.001,
   ntc=1, tol=0.0005, ncorc=1, itimth = 0, ibigm = 1, ishkfl=1, jfastw = 0,
   ntf=1, ntid=0, ntnb=1, nsnb=25, idiel=1, intprt=5,
   cut=15.0, cut2nd=20.0, scnb = 2.0, scee = 1.2, dielc = 1.0,
   ntpr=100, ntwx=10, ntwv=-1, ntwe=10, ioutfm=0, isande=1, iperat=0,
   ntwxm = 999999, ntwvm = 999999, ntwem = 999999,
   ntr=1, ntrx=1, intr=1, iatcmp=1, ntatdp=-1,
   almda = 1.0, almdel = 0.01, isldyn = -3, idifrg = 0,
   nstmeq = 5, nstmul = 5, ndmpmc = 1, idwide = 1,
  &end
set restraints on evaporating waters for glh
1.50
RES 867 867 869 869 872 875 881 881 883 884 895 895
END
END
designating the belly for molecular dynamics
RES 1 6 9 10 22 46 92 104 106 108 111 114 116 127
RES 170 200 206 247 249 250 284 287
RES 296
RES 298 299 312 313 315 328
RES 408
RES 411 412 415 416 419 426 428 429
RES 432
RES 482 555 588 610
RES 612
RES 620 628
RES 645
RES 664 666
RES 685
RES 692
RES 694 695
RES 700
RES 740 745
RES 747
RES 829 830 835 861
RES 864 864 867 867 871 875 878 879 881 881 884 889
RES 892 893 895 895 897 898 900 900 904 906 909 909
RES 913
END
END
  2967 3295 0000 0000 0 0 2 1.00000 0.00000
0610.00000 999.99900 610.00000 2.80000 0 41

  2967 13906 0000 0000 0 0 2 0.00000 1.00000
0610.00000 999.99900 610.00000 2.80000 1 41
----------------------------
I get the following error in the output file:
------------------------------
A "secondary" lambda is defined:
      "Primary" restraints: Translated 0<->1 in 1 windows
      "Secondary" restraints: Translated 0<->1 in 41 windows

                    ----------------------------------------

  Number of triangulated 3-point waters found: 27

  Solute/solvent pointers:
      IPTSOL= 913 NATRCM=14208
      IPTRES= 0 IPTATM= 0
      NSPSOL= 0 NSPSTR= 0
      NSOLUT=14208 NATOM =14208

| Total accumulated time: 2.57 (seconds) / 0.00 (hours)
  %GIBBS-I-NEWRUN, Begining NRUN = 1

2ndary cut: total= 6872834 hbpair= 408 pert= 0 energy= -87.80

  nb-update: total=15802437 hbpair= 820 pert= 0

  NSTEP = 0 TIME(PS) = 0.000 TEMP(K) = 296.383 PRESS = 0.000
  Etotal = -4280.21248 Kinetic = 4958.53563 Potential = -9238.74811
  Bond = 7.11088 Angle = 3010.67736 Dihed = 2505.09809
  1-4 VdW = 1478.59713 1-4 Elec= 11810.72519 Van d Waal = -3664.20881
  Elect. = -24895.44822 H-bond = 0.00000 Constraint = 508.70026
  Ekcmt = 0.00000 VirT = 0.00000 Volume = 0.00000

      Routine TORCON (internal constraints) failed.
      Required change is too large.
      NITER = 7 Bond atom numbers are: 2967 3295

      Routine Sec %
      ----------------------------
| Pairlist 3.99 22.00
| Nonbond 4.35 23.99
| Bond 0.00 0.01
| Angle 0.01 0.04
| Dihedral 0.02 0.11
| PMF 7.09 39.07
| Constraint 0.00 0.01
| Other 2.68 14.78
| Nonsetup 15.65 86.19
       ----------------------------
| Total 18.16 0.01 Hours

| Setup wallclock_t 3 seconds
| Nonsetup wallclock_t 16 seconds

           ***** ERROR TERMINATION DUE TO SHAKE OR TORCON *****
---------------------------

Can anyone please tell me why the primary constraint is varying only 1 window?
How do I make the primary constraint to vary 40 or 100 windows?

With best regards, Asif