AMBER Archive (2002)

Subject: vlimit and vmax

From: Prem Raj (prbj123_at_rediffmail.com)
Date: Fri Sep 20 2002 - 12:27:07 CDT

Dear Amber users,
    I started a dynamics simulation on a protein molecule with
explicit water using Amber 6 ( sander_classic). I am running it on
an sgi iris platform. The initial minimisation ran without
problem. when I started the equilibration md , I get the below
error. How can I rectify this.
should I increase the value of vlimit ( the present value os
15.0)
**********************

  vlimit exceeded for step 0; vmax =
160.0023597269011

      COORDINATE RESETTING (SHAKE) WAS NOT ACCOMPLISHED
      WITHIN 3000 ITERATIONS

       A V E R A G E S O V E R 2 S T E P S

  NSTEP = 2 TIME(PS) = 0.004 TEMP(K) =215744.72 PRESS
=nan
  Etot = nan EKtot = ************ EPtot =
nan
  BOND = 78.1786 ANGLE = 607.3218 DIHED =
967.8024
  1-4 NB = 818.2336 1-4 EEL = 6861.1856 VDWAALS =
nan
  EELEC = nan EHBOND = 0.0000 CONSTRAINT =
719.6468
  EAMBER (non-constraint) = nan
  EKCMT = 1376096.1536 VIRIAL = nan VOLUME =
439846.6328
                                                 Density =
0.8016
  
------------------------------------------------------------------------------

===============================================================================
                       NMR restraints for step 3
  Energy (this step): Bond = 0.000 Angle = 0.000
Torsion = 0.000
  Energy (tot. run) : Bond = 0.000 Angle = 0.000
Torsion = 0.000

  DEVIATIONS: Target=(r2+r3)/2 Target = closer
of r2/r3
             This step Entire run This step
Entire run
            ave. rms ave. rms ave. rms
ave. rms
  Bond 0.000 0.000 0.000 0.000 0.000 0.000
0.000 0.000
  Angle 0.000 0.000 0.000 0.000 0.000 0.000
0.000 0.000
  Torsion 0.000 0.000 0.000 0.000 0.000 0.000
0.000 0.000
===============================================================================

       R M S F L U C T U A T I O N S

  NSTEP = 2 TIME(PS) = 0.004 TEMP(K) =215597.13 PRESS
=nan
  Etot = nan EKtot = ************ EPtot =
nan
  BOND = 6.4372 ANGLE = 49.0044 DIHED =
2.9780
  1-4 NB = 0.3177 1-4 EEL = 4.0132 VDWAALS =
nan
  EELEC = nan EHBOND = 0.0000 CONSTRAINT =
719.6468
  EAMBER (non-constraint) = nan
  EKCMT = 805150.9252 VIRIAL = nan VOLUME =
7049.3470
                                                 Density =
0.0128
  
------------------------------------------------------------------------------

  NMR restraints on final step:

  FATAL ERROR

> >
> >************************************************************
> > > Prem Raj B. Joseph
> > > Dept. of Chemistry and Biochemistry
> > > Howard Hughes Medical Institute
> > > University of Maryland Baltimore County
> > > 1000 Hilltop Circle, Baltimore, MD 21250
> > > Ph: (410)455-2718
> > > email: prem_at_hhmi.umbc.edu, prbj123_at_rediffmail.com
> > >
> > >Residence:
> > > 4747 Drayton Grn
> > > Baltimore, MD - 21227
> > > Ph(Res): (410)247-2413
> >
> >*************************************************************

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