AMBER Archive (2008)

Subject: AMBER: Vlimit Exceeded and inhomogeneous system !!!!!!

From: Piyush Wanjari (ppwanjari_at_gmail.com)
Date: Wed Aug 20 2008 - 23:36:20 CDT

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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