AMBER Archive (2003)

Subject: Re: Sander problem

From: David A. Case (case_at_scripps.edu)
Date: Wed Jun 25 2003 - 17:30:21 CDT

On Tue, Jun 24, 2003, Yuhui Cheng wrote:

> When I used "sander" in Amber7 to do the
> equilibrium simulation of a specific enzyme with IGB =
> 0 in the gas phase, I got the below error:
> " Frac coord min, max: 0.196482015829824 1.00017622911258
> The system has extended beyond
> the extent of the virtual box.

> PS: my input file is as belows:
> "md, npt, warm to 300K quickly,
> &cntrl
> imin = 0, igb = 0,
> ntpr = 100, ntwx = 0,
> ntc = 2, ntf = 2, ntb = 0,
> nstlim = 10000, dt =0.002,
> tempi=10.0, temp0 = 300.0, ntt =1, tautp =2.0,
> ntp = 0, ntr =1, cut = 10.0
> lastrst = 3000000
> &end
> Restrain the heavy atoms
> ..........................."
>

The message means that the system has greatly changed its conformation,
so that it now lies outside a "virtual box" that is 30 Ang. outside the
original conformation.

Since you have set ntr=1, this should never happen. You need to examine
your simulation and energies carefully, and probably visualize the trajectory
to see what is happening. Make sure everything is mimimized first; run
some short trajectories, examine the energies closely, etc.

..good luck....dac 

-- 

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David A. Case                     |  e-mail:      case_at_scripps.edu
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