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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Received on Thu Feb 19 2004 - 14:53:00 PST
