From: Agata Jurkiewicz <>
Date: Fri, 22 Jul 2005 16:09:34 +0200

Dear Amber users,

I run a MD simulation for a small molecule (dUMP) in TIP3P water.
I've tried waterboxes of 6 and 10 A.
I minimized the system before MD to get rid of bad contacts (there
weren't any, anyway).
Then I run 50 ps of MD to heat the system to 300 K. The file
goes like this:

Amber 8, heating
   imin=0, irest=0, ntx=1, ntp=0, nstlim= 25000,
    ntb=1, dt=0.002, ntt=1, temp0=300, tempi=0.1,
    ntpr=50, ntwr=500, scee=1.2, ntf=2, ntc=2,
    cut=12, ntwe=500, ntwx=500, ntave=5000, tautp=2.5,

and the simulation goes OK.

Then I try to equilibrate the system at constant pressure.
The file for equlibration is:
Amber 8, eqlbrtn
   imin=0, irest=1, ntx=7, ntp=1, nstlim= 25000,
    ntb=2, dt=0.002, ntt=1, temp0=300, tempi=300,
    ntpr=50, ntwr=500, scee=1.2, ntf=2, ntc=2,
    cut=12, ntwe=500, ntwx=500, ntave=5000, tautp=2.5,

It goes about 12-17 ps (depending on the size of waterbox) and fails
with a message:
[from md.out file:]

NSTEP = 6300 TIME(PS) = 62.600 TEMP(K) = 479.96 PRESS = 1029.9
  Etot = -3922.0613 EKtot = 2086.3751 EPtot = -6008.4364
  BOND = 8.2350 ANGLE = 16.6152 DIHED = 17.7050
  1-4 NB = 7.1684 1-4 EEL = -107.8100 VDWAALS = 817.9307
  EELEC = -6768.2806 EHBOND = 0.0000 RESTRAINT = 0.0000
  EKCMT = 1007.0906 VIRIAL = 403.0253 VOLUME = 27165.7778
                                                    Density = 0.8072
  Ewald error estimate: 0.1265E-02


  vlimit exceeded for step 6301 ; vmax = 103.896044101908

     Coordinate resetting (SHAKE) was not accomplished
     within 3000 iterations

     Note: This is usually a symptom of some deeper
     problem with the energetics of the system.

I viewed all the trajectories in VMD and didn't see anything unusual
in the geometry of the system.
I tried this calculation on a different machine, with the same result.
I've used the same input files to run MD for a protein-ligand system,
with the same ligand, successfully.
I will appreciate any hints.


Agata Jurkiewicz
Quantum Chemistry Laboratory
Faculty of Chemistry, Warsaw University
Pasteura 1, 02-093 Warsaw, Poland
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Received on Fri Jul 22 2005 - 15:53:00 PDT
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