AMBER Archive (2004)

Subject: Re: AMBER: pmf calculation using gibbs.

From: Myunggi Yi (my02c_at_fsu.edu)
Date: Thu Feb 19 2004 - 09:13:30 CST

Thank you Dr. Case

Now, I have anothe porblem.

$ [0] MPI Abort by user Aborting program !
[0] Aborting program!
p0_2458: p4_error: : 1

[1] Exit 1 gibbs -O -i umb.in -o s1.out -p mth.top
-c md1.restrt -r s1.restrt -x s1.mdcrd

This is error message, and the following is output file.

FEP two methanes PMF
&cntrl
                                                                               
ntx=1,
ntb=2,
ntp=1,
ntt=5,
                                                                               
dt=0.002,
                                                                               
                                                                               
nstlim=20000,
nstmeq=4000,
nstmul=16000,
temp0=300.0,
ntc=2,
ntf=2,
                                                                               
ncorc=1,
                                                                               
cut=9.0,
intprt=0,
                                                                               
ntpr=100,
ntwx=100,
ntwe=100,
                                                                               
nrun=41,
almda=1.0,
almdel=0.1,
isldyn=-3,
ielper=0,
intr=1,
scnb=2.0, scee=1.2,
&end
    1 6 0 0 1 0 1 1.00000 0.00000
   5.00000 8.00000 5.00000 8.00000 0 0
                                                                               
-------------------------------------------------------------------------------

                   READING MOLECULAR TOPOLOGY FILE (PPARM)

| New format PARM file being parsed.
| Version = 1.000 Date = 01/28/04 Time = 14:57:41
                             --------------------
                                DYNAMIC MEMORY
                                  ALLOCATED USED
| INTEGER: 3750000 33557
| REAL: 1500000 95211
| CHARACTER: 125000 8140

| AVAILABLE INTEGER WORDS x 1 N-B PAIRS/WORD = 3716443 MAXIMUM N-B PAIRS
                             --------------------

 Title line from parm:
 MTH

                          CONTROL FLAGS FOR THIS RUN
                          --------------------------

FEP two methanes PMF

     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 = 1216
     NSM = 0 NRAM = 0 NTX = 1
     NTXO = 1 ISEED = 71277
     TempI = 0.000 HEAT = 0.000

     NTB = 2 IFTRES= 1 BOXX = 29.637
     BOXY = 25.372 BOXZ = 27.481 BETA = 90.000

     NRUN = 41 NTT = 5 TEMP0 = 300.000
     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= 20000 INIT = 3
     T = 0.00000 DT = 0.00200
     VLIMIT= 0.000 IVEMAX= 0

     NTC = 2
     TOL = 0.00050 TOLR2 = 0.00010
     NCORC = 1 ISHKFL= 1 ITIMTH= 0
     JFASTW= 0

     NTF = 2 NTID = 0
     NTNB = 1 NSNB = 50 IDIEL = 1
     IELPER= 0 IMGSLT= 0 IDSX0 = 0
     ITRSLU= 1
     IOLEPS= 0 INTPRT= 0 ITIP = 0

     CUT = 9.00000 SCNB = 2.00000
     SCEE = 1.20000 DIELC = 1.00000
     CUT2ND= 0.00000 CUTPRT= 0.00000

     NTPR = 100 NTWX = 100 NTWV = -1
     NTWE = 100 NTWXM = 999999 NTWVM = 999999
     NTWEM = 999999 IOUTFM= 0
     ISANDE= 0 IPERAT= 0 IATCMP= 0
     NTATDP= 0 ICMPDR= 0 NCMPDR= 0
     NTWPRT= 0 NTWPR0= 0

     NTR = 0 NRC = 0 NTRX = 1
     TAUR = 1.000 INTR = 1 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= 4000 NSTMUL= 16000 NDMPMC= 0
     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: MTH

                   READING INTERNAL RESTRAINTS/CONSTRAINTS:
                   ----------------------------------------

 C1 ( 1)-C1 ( 6) :
     IUMB=1 IZE=0 ITOR=1 IPER= 0 IPER2= 0 LAM1= 1.000 LAM2= 0.000
     K1= 5.0000 Req1= 8.0000 K2= 5.0000 Req2= 8.0000
                   ----------------------------------------

 Number of triangulated 3-point waters found: 402

 Solute/solvent pointers:
     IPTSOL= 2 NATRCM= 10
     IPTRES= 0 IPTATM= 0
     NSPSOL= 3 NSPSTR= 10
     NSOLUT= 10 NATOM = 1216

| Total accumulated time: 0.21 (seconds) / 0.00 (hours)
 %GIBBS-I-NEWRUN, Begining NRUN = 1

 NSTEP = 0 TIME(PS) = 0.000 TEMP(K) = 0.000 PRESS =
**********
 Etotal = ************ Kinetic = 0.00000 Potential = ************
 Bond = 0.00000 Angle = 1.18748 Dihed = 0.00000
 1-4 VdW = 0.00000 1-4 Elec= 0.00000 Van d Waal = ************
 Elect. = -1436.85936 H-bond = 0.00000 Constraint = 0.00000
 Ekcmt = 0.00000 VirT = ************ Volume = 20663.92973
                                                 Density = 0.58458

 Internal UMBRELLA restraints defined in Gibbs (not inc. in above):
 Bond = 155.95417 Angle = 0.00000 Torsion= 0.00000

     COORDINATE RESETTING CANNOT BE ACCOMPLISHED,
     DEVIATION IS TOO LARGE
     NITER, NIT, LL, I AND J ARE : 0 0 3 1 4

     Routine Sec %
     ----------------------------
| Pairlist 0.02 8.03
| Nonbond 0.01 5.69
| Bond 0.00 0.00
| Angle 0.00 0.02
| Dihedral 0.00 0.00
| PMF 0.00 0.00
| Constraint 0.00 0.12
| Other 0.22 86.15
| Nonsetup ******************
      ----------------------------
| Total 0.25 0.00 Hours

| Setup wallclock_t 0 seconds
| Nonsetup wallclock_t 0 seconds

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

     AMBER/MPI: ERRORS ENCOUNTERED

I couldn't find any information from Amber Archive.
What is the problem?
Thanks again. 

-- 
Best wishes,

Myunggi Yi
===========================================
KLB 419
Institute of Molecular Biophysics
Florida State University
Tallahassee, FL. 32306

(850) 645-1334
http://www.csit.fsu.edu/~myunggi
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