AMBER Archive (2008)

Subject: AMBER: multiple dihedral restraints using group (in Amber 10)

From: mkseo (
Date: Tue Jun 17 2008 - 16:00:50 CDT

Hello Amber users,

I tried to calculate the potential of mean force of the dissociation
of protein-sugar complex using umbrella sampling.
I added six restraint potentials (distance, angles and dihedral
restraints) with defining by a group of atoms. (this kind of restraint
is provided in Amber 10)

The magnitude of the force constants for each restraint potential was
estimated from the fluctuations of its associated coordinates as k_x =
k_BT/<delta x^2>.
Langevin thermostat was used to maintain constant temperature (see the
input below)

Dynamic Simulation with Constant Temperature
   ntwe =500, ntwx =500, ntwv =500, ntpr =500,
   ntt =3, temp0 =300.0, tempi =300.0,
   gamma_ln = 60.0,
   scnb = 2.0, scee = 1.2,
   ntb =0, ntc =2, ntf =1, cut=9999.0,
   nstlim =150000, dt =0.001,
   irest =1, ntx =5,
   nmropt =1,
  &wt type ='DUMPFREQ', istep1=1 /
  &wt type='END' /
DUMPAVE = native_T300_d_vs_t.5.0

But, I have the following error message.

The system has extended beyond
      the extent of the virtual box.
  Restarting sander will recalculate
     a new virtual box with 30 Angstroms
     extra on each side, if there is a
     restart file for this configuration.
  SANDER BOMB in subroutine Routine: map_coords (ew_force.f)
  Atom out of bounds. If a restart has been written,
  restarting should resolve the error

Can anyone help to solve this problem?
What is wrong with my simulation, force constants or thermostat



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