AMBER Archive (2004)

Subject: Re: AMBER: long minimization in sander

From: MURAT CETINKAYA (cetinkayam_at_psu.edu)
Date: Mon Oct 25 2004 - 10:32:10 CDT

Sorry, I am pasting the files now...
This is the case for 1ns 300K vacuum MD for a protein

This is MDin file:
1ns vacuum MD
 &cntrl
  imin = 0, ntb = 0,
  ntpr = 5000, ntwx = 1000, ntwr = 1000,
  ntt = 1, ntp = 0,
  tempi = 0.0, temp0 = 300.0,
  nstlim = 1000000,
  cut = 10.0
 &end

and I get the following output message just at the instant of 0 ps of MD:

Frac coord min, max: -3.26662690012118D-004 0.826317897389839
[12] MPI Abort by user Aborting program !
 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.
 EWALD BOMB in subroutine Routine: map_coords (ew_force.f)
 Atom out of bounds. If a restart has been written,
 restarting should resolve the error
[2] MPI Abort by user Aborting program !
[2] Aborting program!

Actually, I do not understand why this happens at 300K ?

Thanks.

On Mon, 25 Oct 2004 08:09:49, Bill Ross wrote:

> > The problem is: I have made 2000O steps of min prior to my 1ns MD at
> > 600K and it worked good. However, I wanted to use my same minimized
> > system prior to my 300K MD but it just terminates at the beginning.
>
> With what mdin? With what output message?
>
> > This happens both in vacuum and explicit solvent environment...
> >
> > any ideas?
>
> Mistake in mdin or choice of inpcrd,prmtop for running sander.
>
> Bill
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Murat CETINKAYA
Biomolecular Materials Lab,
Dept. of Engr. Science and Mechanics,
The Pennsylvania State University,
University Park, PA 16802
office: (814) 863 9967
web: www.personal.psu.edu/muc176
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