AMBER Archive (2002)

Subject: Re: vlimit and vmax

From: darden (darden_at_gamera.niehs.nih.gov)
Date: Fri Sep 20 2002 - 14:27:10 CDT

Dear Prem
Your problem looks too severe for a vlimit fix. It looks like you started
with 2 atoms essentially on top of each other. Note vdwaals and
electrostat are both nan which indicates a divide by zero in the
coulombs law or the 6-12 term. The easiest way this can happen is when the
box size is somehow inappropriate so that periodic imaging leads to atoms
(usually waters) on top of each other. One way to check is to set the box
size a little bigger (say 0.5 angstroms in all three directions) and see
if the problem is alleviated.
good luck
Tom
 On 20 Sep 2002, Prem Raj wrote:

> 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
> > >
> > >*************************************************************
>
>
> ****************************
> "Everyday is the first day of the rest of your life"
>
> Dept. of Crystallography and Biophysics
> University of Madras
> Guindy Campus
> Chennai 600 025
> India
> phone: 091 44 2300122, tele fax: 091 44 2300122
>
> House Address:
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> ****************************
>