I'm trying to run a PMF symulation with gibbs (probably you have
received several messages from me concerning gibbs).
Last time I had a problem with convergence in TORCON routine
" Routine TORCON (internal constraints) failed
to converge within 1000 iterations.
Error from TORCON while imposing loop constraints at lambda+d_lambda
or lambda-d_lambda"
Now I have changed the way for defining restraints and the error
message has changed (I don't know if for better or worse).
" Routine TORCON (internal constraints) failed.
Required change is too large.
NITER = 14 Bond atom numbers are: 128 130
Error from TORCON while imposing loop constraints at lambda+d_lambda
or lambda-d_lambda"
Could anybody tell me what this means and how can I solve it? At the end
of the message is the complete output file.
Thank you in advance,
Miguel.
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
---------------------------------------
GIBBS Version 5 AMBER/UCSF(1997)
--------------------------------------
[-O]verwriting output
File Assignments:
-----------------
|PIN : 210pmf.in
|POUT : abn210pmf.out
|PCOORD : abn210pmf.trj
|PVEL : PVEL
|PEN : PEN
|PPARM : ../6leap/abn210.top
|PINCRD : abn202dm2.rst
|PREFC : PREFC
|PREST : abn210pmf.rst
|PINFO : abn210pmf.inf
|MICSTAT : abn210pmf.mic
|CONSTMAT: abn210pmf.ctm
|CNSTSCRT: abn210pmf.cst
|PATNRG : PATNRG
Here is the input file:
Calculo de Perturbación de Energía Libre (FEP)
Temperatura constante 298k
Presion constante
&cntrl
ntx=1, ntb=2, intr=2, ntwx=1000,
ntt=1, temp0=298.0, tautp=0.2,
ntp=1, taup=0.2, isvat=1,
nstlim=-1,
ntc=2, scee=1.2,
ntpr=100, ntpr=100, ntwprt=-1,
ncorc=1,
almdel=0.1, isldyn=-3, nstmeq=5, nstmul=5,
ndmpmc=100,
&end
21 127 84 0 1 1 2 1.00000 0.00000
100.00000 180.00000 100.00000 180.00000
21 127 0 0 1 1 2 1.00000 0.00000
100.00000 4.17000 100.00000 4.17000
128 127 0 0 0 0 2 1.00000 0.00000
10.0000 8.07000 10.0000 20.00000
-------------------------------------------------------------------------------
READING MOLECULAR TOPOLOGY FILE (PPARM)
| New format PARM file being parsed.
| Version = 1.000 Date = 12/09/02 Time = 15:24:28
--------------------
DYNAMIC MEMORY
ALLOCATED USED
| INTEGER: 3750000 241854
| REAL: 1500000 628967
| CHARACTER: 125000 61536
| AVAILABLE INTEGER WORDS x 1 N-B PAIRS/WORD = 3508146 MAXIMUM N-B
PAIRS
--------------------
Title line from parm:
CONTROL FLAGS FOR THIS RUN
--------------------------
Calculo de Perturbación de Energía Libre (FEP)
THE TIME LIMIT FOR THE JOB = 1000000.
THE RESTART PARAMETER = 0 (irest )
THE FLAG FOR BELLY OPTION = 0 (ibelly)
THE FLAG FOR DNA CHARGE CHANGE = 0 (ichdna)
THE FLAG FOR POLARIZATION = 0 (ipol )
THE FLAG FOR 3bods = 0 (i3bod )
# of atoms = 9239
NSM = 0 NRAM = 0 NTX = 1
NTXO = 1 ISEED = 71277
TempI = 0.000 HEAT = 0.000
NTB = 2 IFTRES= 1 BOXX = 51.627
BOXY = 49.032 BOXZ = 48.997 BETA = 90.000
NRUN = 1 NTT = 1 TEMP0 = 298.000
DTEMP = 10.000 TAUTP = 0.200 TAUTS = 0.200
ISOLVP= 0 NSEL = 0 DTUSE = 1.000
NTP = 1 NPSCAL= 0 PRES0 = 1.000
COMP = 44.600 TAUP = 0.200
NTCM = 0 NSCM = 90000000
ISVAT = 1
NSTLIM=******* INIT = 3
T = 0.00000 DT = 0.00100
VLIMIT= 0.000 IVEMAX= 0
NTC = 2
TOL = 0.00050 TOLR2 = 0.00010
NCORC = 1 ISHKFL= 1 ITIMTH= 0
JFASTW= 0
NTF = 1 NTID = 0
NTNB = 1 NSNB = 50 IDIEL = 1
IELPER= 0 IMGSLT= 0 IDSX0 = 0
ITRSLU= 1
IOLEPS= 0 INTPRT= 0 ITIP = 0
CUT = 8.00000 SCNB = 2.00000
SCEE = 1.20000 DIELC = 1.00000
CUT2ND= 0.00000 CUTPRT= 0.00000
NTPR = 100 NTWX = 1000 NTWV = -1
NTWE = -1 NTWXM = 999999 NTWVM = 999999
NTWEM = 999999 IOUTFM= 0
ISANDE= 0 IPERAT= 0 IATCMP= 0
NTATDP= 0 ICMPDR= 0 NCMPDR= 0
NTWPRT= -1 NTWPR0= 0
NTR = 0 NRC = 0 NTRX = 1
TAUR = 1.000 INTR = 2 IBIGM = 1
IDUM1 = 0 NMRMAX= 0 IWTMAX = 0
ISFTRP= 0 RWELL = 5.00000
IFTIME= -1 CTIMT = 0.00000
ALMDA = 1.0000000 ALMDEL = 0.1000000
ISLDYN= -3 IDIFRG= 0
NSTMEQ= 5 NSTMUL= 5 NDMPMC= 100
IDWIDE= 0 IBNDLM= 0
IFTIME= 0 CTIMT =
NSTPE = 2 NSTPA = 2
DTE = 0.00100 DTA = 0.00100
IVCAP = 0 MATCAP= 0 IFCAP = 0
NATCAP= 0 CUTCAP= 0.00000
XCAP = 0.00000 YCAP = 0.00000
ZCAP = 0.00000 FCAP = 1.50000
Water definition for fast 3pt model:
Resname = WAT ; Oxygen_name = O ; Hyd_name1 = H1 ; Hyd_name2 =
H2
------------------
CALCULATION METHOD
Fixed-width window Free Energy Perturbation
Delta_lambda = 0.1000000; Simulation direction 1->0
------------------
READING ATOMIC COORDINATES AND VELOCITIES
-----------------------------------------
Title:
READING INTERNAL RESTRAINTS/CONSTRAINTS:
----------------------------------------
O4 ( 21)-D1 ( 127)-O4 ( 84) :
IUMB=1 IZE=0 ITOR=2 IPER= 0 IPER2= 0 LAM1= 1.000 LAM2= 0.000
K1= 100.0000 Req1= 180.0000 K2= 100.0000 Req2= 180.0000
O4 ( 21)-D1 ( 127) :
IUMB=1 IZE=0 ITOR=2 IPER= 0 IPER2= 0 LAM1= 1.000 LAM2= 0.000
K1= 100.0000 Req1= 4.1700 K2= 100.0000 Req2= 4.1700
N01 ( 128)-D1 ( 127) :
IUMB=0 IZE=0 ITOR=2 IPER= 0 IPER2= 0 LAM1= 1.000 LAM2= 0.000
K1= 10.0000 Req1= 8.0700 K2= 10.0000 Req2= 20.0000
----------------------------------------
Note: Constrained bond ( 21- 127) is part of a ring
Note: Constrained angle ( 21- 127- 84) is part of a ring
Number of triangulated 3-point waters found: 3025
Solute/solvent pointers:
IPTSOL= 8 NATRCM= 164
IPTRES= 0 IPTATM= 0
NSPSOL= 4 NSPSTR= 164
NSOLUT= 9239 NATOM = 9239
| Total accumulated time: 2.57 (seconds) / 0.00 (hours)
%GIBBS-I-NEWRUN, Begining NRUN = 1
Routine TORCON (internal constraints) failed.
Required change is too large.
NITER = 14 Bond atom numbers are: 128 130
Error from TORCON while imposing loop constraints at lambda+d_lambda
or lambda-d_lambda
Received on Thu Jan 09 2003 - 02:11:41 PST
