Hi all,
I am trying to simulate a bowl-shaped macromolecule with 10 United atom
methane and 1000 tip4p-ew water molecules, where 6 Na+ atoms are added to
make macromolecule neutral.
Minimiztion (inp1) goes fine, but when i start equilibarion (NVT)(inp2),
vlimit exceeds and shows folowing messages
| Local SIZE OF NONBOND LIST = 41794
| TOTAL SIZE OF NONBOND LIST = 559211
***** Processor 0
***** System must be very inhomogeneous.
***** Readjusting recip sizes.
In this slab, Atoms found: 724 Allocated: 700
NSTEP = 6800 TIME(PS) = 6.800 TEMP(K) = 304.12 PRESS =
0.0
Etot = -9582.4333 EKtot = 1995.2365 EPtot =
-11577.6698
BOND = 81.7912 ANGLE = 109.6310 DIHED =
133.5732
1-4 NB = 80.2475 1-4 EEL = -755.0708 VDWAALS =
1959.7924
EELEC = -13187.6343 EHBOND = 0.0000 RESTRAINT =
0.0000
Ewald error estimate: 0.8471E-05
------------------------------------------------------------------------------
NSTEP = 6900 TIME(PS) = 6.900 TEMP(K) = 304.47 PRESS =
0.0
Etot = -9583.2823 EKtot = 1997.5177 EPtot =
-11580.8000
BOND = 68.6413 ANGLE = 134.3476 DIHED =
132.1145
1-4 NB = 85.7959 1-4 EEL = -772.9748 VDWAALS =
1931.4358
EELEC = -13160.1603 EHBOND = 0.0000 RESTRAINT =
0.0000
Ewald error estimate: 0.1485E-03
------------------------------------------------------------------------------
vlimit exceeded for step 6923 ; vmax = 332.733246702116
vlimit exceeded for step 6924 ; vmax = 24.7292698719054
vlimit exceeded for step 6925 ; vmax = 22.4036737711972
vlimit exceeded for step 6927 ; vmax = 21.8790257202111
vlimit exceeded for step 6928 ; vmax = 22.7903070570842
vlimit exceeded for step 6929 ; vmax = 20.3426835178755
vlimit exceeded for step 6938 ; vmax = 20.9046347001600
vlimit exceeded for step 6943 ; vmax = 24.9676557381340
Here are the input files:
inp1
&cntrl
imin=1, maxcyc = 50000, ncyc = 30000,
ntx=1, irest=0, ntpr=100, ntwr=500, ntwx=500,
ntwe=500, ntf=1, ntb=1, ntc=1
dt=0.001, ig=323657
&end
&ewald
ew_type=0, dsum_tol=0.000001
&end
END
inp2
&cntrl
imin=0, ntx=1, irest=0, ntpr=100, ntwr=1000, ntwx=100,
ntwe=500, ntf=2, ntb=1, nstlim=100000,
temp0 = 300.0, tempi=300.0, ntt=2, tautp=1.0,
ntp=0,
ntc=2,
dt=0.001, ig=323656
&end
&ewald
ew_type=0, dsum_tol=0.000001
&end
END
inp3 (equilibration NPT)
&cntrl
imin=0, ntx=1, irest=0, ntpr=100, ntwr=10000, ntwx=1000,
ntwe=500, ntf=2, ntb=2, nstlim=1000000,
temp0 = 300.0, tempi=300.0, ntt=2, tautp=1.0,
ntp=1, pres0=1, comp=44.6,
taup=2.0, ntc=2,
dt=0.001, ig=323656
&end
&ewald
ew_type=0, dsum_tol=0.000001
&end
END
inp4 (final production run NPT)
&cntrl
imin=0, ntx=5, irest=1, ntpr=1000, ntwr=10000, ntwx=100,
ntwe=500, ntf=2, ntb=2, nstlim=10000000,
temp0 = 300.0, tempi=300.0, ntt=2, tautp=1.0,
ntp=1, pres0=1, comp=44.6,
taup=2.0, ntc=2,
dt=0.001, ig=323656
&end
&ewald
ew_type=0, dsum_tol=0.000001
&end
END
Please tell me how to solve the vlimit exceed problem and inhomogeneousness
of system.
Thanks
Piyush Wanjari
Graduate Student
Tulane University
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Received on Sun Aug 24 2008 - 06:07:26 PDT
