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
--
==================================================================
David A. Case | e-mail: case.scripps.edu
Dept. of Molecular Biology, TPC15 | fax: +1-858-784-8896
The Scripps Research Institute | phone: +1-858-784-9768
10550 N. Torrey Pines Rd. | home page:
La Jolla CA 92037 USA | http://www.scripps.edu/case
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Received on Wed Jun 25 2003 - 23:53:01 PDT
