AMBER Archive (2009)

Subject: Re: [AMBER] please help me out

From: Hugh Heldenbrand (helde010_at_umn.edu)
Date: Wed Apr 08 2009 - 10:44:54 CDT

Ross and Bharat-

I have recently been doing many hundreds of minimizations of a small
molecule systems, and I see this error for probably one out of every
hundred minimizations that I do. I won't comment on the stability of a
protein in the gas phase, but my solution to this particular error is to
restart the minimization with a number steps smaller than the number
that it took to fail. This will successfully produce a restart file
that I can use to keep minimizing for however many steps that I want to
(presumably the second minimization does not exceed its new virtual box).

-Hugh Heldenbrand
Graduate Student
Chemistry Dept.
University of Minnesota

Ross Walker wrote:
> Hi Bharat,
>
> You are running a gas phase simulation. This means one of two things have
> occurred. The first is that your system may have blown up because it is
> unstable in a vacuum at 300K like most proteins are in reality. The second
> is that your system has diffused too far away from the origin which it will
> do in gas phase if you don't remove center of mass rotation and translation.
>
> However, the strange thing is that your input file suggests you are doing a
> minimization and I have never seen this error before for a minimization
> since this typically doesn't change the coordinates much. My guess though is
> that either this is not the input file you used or your initial system is
> really high in energy due to the structure being bad. You should probably
> start with this.
>
> Good luck,
> Ross
>
> -----Original Message-----
> From: amber-bounces_at_ambermd.org [mailto:amber-bounces_at_ambermd.org] On Behalf
> Of bharat lakhani
> Sent: Wednesday, April 08, 2009 2:19 AM
> To: AMBER Mailing List
> Subject: [AMBER] please help me out
>
> respected sir,
> when i am running sander.I am getting following error
>
>
> Frac coord min, max: -125660551.867471 125660552.914482
> 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
>
>
>
>
> For minimization i am giving these parameters
>
>
> in vacuo minimization
> &cntrl
> imin = 1,
> maxcyc = 1000,
> ncyc = 200,
> ntb = 0,
> igb = 0,
> cut = 12
> /
> _______________________________________________
> AMBER mailing list
> AMBER_at_ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
>
> _______________________________________________
> AMBER mailing list
> AMBER_at_ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>

_______________________________________________
AMBER mailing list
AMBER_at_ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber