Dear amber users,
I have installed amber10 and pmemd in altix4700.
All the installation went well without error after guidance from amber mailing list.
If I run sander.MPI in amber10, it runs fine, but if I run pmemd it run very slow. I run my script not using PBS but directly.
Here I give my *.in file and the *.out file contents.
*in file
=========Dynamic Simulation with Constant Pressure
&cntrl
imin=0,
irest=1, ntx=7,
iwrap = 1, ntxo=1,
scnb=1.0, scee=1.0,
ntt=3, gamma_ln = 1.0,
tempi = 300.0, temp0=300.0, tautp=0.2,
ntb = 2, ntp=1, taup=0.2,
ntf=2,ntc=2,
nstlim=100000, dt=0.001,
ntwe=100, ntwx=100, ntpr=100, ntwr=-50000,
ntr=0,
/
*.out
============
-------------------------------------------------------
Amber 10 SANDER 2008
-------------------------------------------------------
| PMEMD implementation of SANDER, Release 10
| Run on 05/14/2009 at 13:32:03
[-O]verwriting output
File Assignments:
| MDIN: MD-betaMalto-lowLyo.in
| MDOUT: betaMalto-lowLyo-MD00-run0000.out
| INPCRD: e2malto-lowLyo-equi21.rst_100000
| PARM: maltose-lowLyo.top
| RESTRT: betaMalto-lowLyo-MD01-run0100.rst
| REFC: refc
| MDVEL: mdvel
| MDEN: mden
| MDCRD: betaMalto-lowLyo-MD00-run0000.traj
| MDINFO: mdinfo
|LOGFILE: logfile
Here is the input file:
Dynamic Simulation with Constant Pressure
&cntrl
imin=0,
irest=1, ntx=7,
iwrap = 1, ntxo=1,
scnb=1.0, scee=1.0,
ntt=3, gamma_ln = 1.0,
tempi = 300.0, temp0=300.0, tautp=0.2,
ntb = 2, ntp=1, taup=0.2,
ntf=2,ntc=2,
nstlim=100000, dt=0.001,
ntwe=100, ntwx=100, ntpr=100, ntwr=-50000,
ntr=0,
/
| Conditional Compilation Defines Used:
| MPI
| SLOW_INDIRECTVEC
| PUBFFT
| MKL
| Largest sphere to fit in unit cell has radius = 24.102
| New format PARM file being parsed.
| Version = 1.000 Date = 06/23/08 Time = 17:06:22
| Duplicated 0 dihedrals
| Duplicated 0 dihedrals
--------------------------------------------------------------------------------
1. RESOURCE USE:
--------------------------------------------------------------------------------
getting new box info from bottom of inpcrd
NATOM = 23736 NTYPES = 9 NBONH = 14776 MBONA = 9216
NTHETH = 27648 MTHETA = 12032 NPHIH = 45312 MPHIA = 21248
NHPARM = 0 NPARM = 0 NNB = 123552 NRES = 1256
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: 18 9 10
| Direct force subcell size = 5.1696 5.3561 5.0569
BOX TYPE: RECTILINEAR
--------------------------------------------------------------------------------
2. CONTROL DATA FOR THE RUN
--------------------------------------------------------------------------------
General flags:
imin = 0, nmropt = 0
Nature and format of input:
ntx = 7, 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 = 8.00000, intdiel = 1.00000
scnb = 1.00000, scee = 1.00000
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
Langevin dynamics temperature regulation:
ig = 71277
temp0 = 300.00000, tempi = 300.00000, gamma_ln= 1.00000
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 = 93.053 Box Y = 48.205 Box Z = 50.569
Alpha = 90.000 Beta = 90.000 Gamma = 90.000
NFFT1 = 96 NFFT2 = 50 NFFT3 = 54
Cutoff= 8.000 Tol =0.100E-04
Ewald Coefficient = 0.34864
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 = 4012.500 ps
Number of triangulated 3-point waters found: 1000
Sum of charges from parm topology file = 0.00000000
Forcing neutrality...
| Dynamic Memory, Types Used:
| Reals 908174
| Integers 1893246
| Nonbonded Pairs Initial Allocation: 168376
| 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
---------------------------------------------------
NSTEP = 100 TIME(PS) = 4012.600 TEMP(K) = 301.34 PRESS = -45.6
Etot = 72323.5211 EKtot = 16896.3909 EPtot = 55427.1302
BOND = 4331.7919 ANGLE = 12660.8451 DIHED = 3557.8100
1-4 NB = 5543.6944 1-4 EEL = 112668.1311 VDWAALS = -10250.7744
EELEC = -73084.3679 EHBOND = 0.0000 RESTRAINT = 0.0000
EKCMT = 1136.7441 VIRIAL = 1359.7065 VOLUME = 226657.6514
Density = 1.0897
Ewald error estimate: 0.1325E-03
------------------------------------------------------------------------------
NSTEP = 200 TIME(PS) = 4012.700 TEMP(K) = 300.36 PRESS = 51.9
Etot = 72308.4304 EKtot = 16841.3962 EPtot = 55467.0342
BOND = 4223.5093 ANGLE = 12742.0334 DIHED = 3598.7024
1-4 NB = 5569.0962 1-4 EEL = 112679.4301 VDWAALS = -10228.2235
EELEC = -73117.5137 EHBOND = 0.0000 RESTRAINT = 0.0000
EKCMT = 1124.6180 VIRIAL = 870.8898 VOLUME = 226443.8438
Density = 1.0907
Ewald error estimate: 0.8322E-04
------------------------------------------------------------------------------
I dont know what is the error.
Can anyone help?
Thank you in advance.
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 Wed May 20 2009 - 16:27:19 PDT
