Dear Amber Experts,
I have have been using AMBER10 for my simulation. For the equilibrium process I use sander.MPI and for the production process I tried to use PMEMD. What is happening is the simulation terminates immediately upon submitted. The message in the output file is as below:
-------------------------------------------------------
Amber 10 SANDER 2008
-------------------------------------------------------
| PMEMD implementation of SANDER, Release 10
| Run on 09/28/2010 at 17:50:00
[-O]verwriting output
File Assignments:
| MDIN: MD-malto-highLyo4800A10.in
| MDOUT: malto-highLyo4800-MD00-run1000.out
| INPCRD: e1malto-highLyo4800-Cp38.rst_100000
| PARM: malto-highLyo4800.top
| RESTRT: malto-highLyo4800-MD01-run0100.rst
| REFC: refc
| MDVEL: mdvel
| MDEN: mden
| MDCRD: malto-highLyo4800-MD00-run1000.traj
| MDINFO: mdinfo
|LOGFILE: logfile
Here is the input file:
Dynamic Simulation with Constant Pressure
&cntrl
imin=0,
irest=1, ntx=5,
scnb=1.0, scee=1.2,
iwrap = 1, nscm=1000,
ntt=2, temp0=348.0, tautp=1.0,
ntb = 2, ntp=1, taup=0.2,
ntf=2,ntc=2,
nstlim=100000, dt=0.001,
ntwe=100, ntwx=100, ntpr=100, ntwr=-50000,
cut = 9.0
/
| Conditional Compilation Defines Used:
| MPI
| SLOW_INDIRECTVEC
| PUBFFT
| MKL
| Largest sphere to fit in unit cell has radius = 26.401
| New format PARM file being parsed.
| Version = 1.000 Date = 07/09/10 Time = 18:22:02
| Duplicated 0 dihedrals
| Duplicated 0 dihedrals
--------------------------------------------------------------------------------
1. RESOURCE USE:
--------------------------------------------------------------------------------
getting new box info from bottom of inpcrd
NATOM = 35136 NTYPES = 9 NBONH = 26176 MBONA = 9216
NTHETH = 27648 MTHETA = 12032 NPHIH = 45312 MPHIA = 21248
NHPARM = 0 NPARM = 0 NNB = 138752 NRES = 5056
NBONA = 9216 NTHETA = 12032 NPHIA = 21248 NUMBND = 9
NUMANG = 14 NPTRA = 20 NATYP = 9 NPHB = 1
IFBOX = 1 NMXRS = 81 IFCAP = 0 NEXTRA = 0
NCOPY = 0
| Coordinate Index Table dimensions: 21 9 10
| Direct force subcell size = 5.5495 5.8669 5.9727
BOX TYPE: RECTILINEAR
--------------------------------------------------------------------------------
2. CONTROL DATA FOR THE RUN
--------------------------------------------------------------------------------
General flags:
imin = 0, nmropt = 0
Nature and format of input:
ntx = 5, irest = 1, ntrx = 1
Nature and format of output:
ntxo = 1, ntpr = 100, ntrx = 1, ntwr = -50000
iwrap = 1, ntwx = 100, ntwv = 0, ntwe = 100
ioutfm = 0, ntwprt = 0, idecomp = 0, rbornstat= 0
Potential function:
ntf = 2, ntb = 2, igb = 0, nsnb = 25
ipol = 0, gbsa = 0, iesp = 0
dielc = 1.00000, cut = 9.00000, intdiel = 1.00000
scnb = 1.00000, scee = 1.20000
Frozen or restrained atoms:
ibelly = 0, ntr = 0
Molecular dynamics:
nstlim = 100000, nscm = 1000, nrespa = 1
t = 0.00000, dt = 0.00100, vlimit = 20.00000
Anderson (strong collision) temperature regulation:
ig = 71277, vrand = 1000
temp0 = 348.00000, tempi = 0.00000
Pressure regulation:
ntp = 1
pres0 = 1.00000, comp = 44.60000, taup = 0.20000
SHAKE:
ntc = 2, jfastw = 0
tol = 0.00001
| Intermolecular bonds treatment:
| no_intermolecular_bonds = 1
| Energy averages sample interval:
| ene_avg_sampling = 100
Ewald parameters:
verbose = 0, ew_type = 0, nbflag = 1, use_pme = 1
vdwmeth = 1, eedmeth = 1, netfrc = 1
Box X = 116.539 Box Y = 52.802 Box Z = 59.727
Alpha = 90.000 Beta = 90.000 Gamma = 90.000
NFFT1 = 120 NFFT2 = 54 NFFT3 = 60
Cutoff= 9.000 Tol =0.100E-04
Ewald Coefficient = 0.30768
Interpolation order = 4
| PMEMD ewald parallel performance parameters:
| block_fft = 1
| fft_blk_y_divisor = 4
| excl_recip = 0
| excl_master = 0
| atm_redist_freq = 320
--------------------------------------------------------------------------------
3. ATOMIC COORDINATES AND VELOCITIES
--------------------------------------------------------------------------------
begin time read from input coords = 1950.000 ps
Number of triangulated 3-point waters found: 4800
Sum of charges from parm topology file = 0.00000000
Forcing neutrality...
| Dynamic Memory, Types Used:
| Reals 1317014
| Integers 2236056
| Nonbonded Pairs Initial Allocation: 331018
| Running AMBER/MPI version on 64 nodes
--------------------------------------------------------------------------------
4. RESULTS
--------------------------------------------------------------------------------
---------------------------------------------------
APPROXIMATING switch and d/dx switch using CUBIC SPLINE INTERPOLATION
using 5000.0 points per unit in tabled values
TESTING RELATIVE ERROR over r ranging from 0.0 to cutoff
| CHECK switch(x): max rel err = 0.3338E-14 at 2.509280
| CHECK d/dx switch(x): max rel err = 0.8261E-11 at 2.768360
---------------------------------------------------
Coordinate resetting (shake) was not accomplished
within 3000 iterations
###########################################################################
Could anyone help me indicate why this happens when using pmemd?
Thank you.
Vijay.M
Vijay Manickam Achari
(Phd Student c/o Prof Rauzah Hashim)
Chemistry Department,
University of Malaya,
Malaysia
vjramana.gmail.com
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Received on Tue Sep 28 2010 - 02:30:04 PDT
