What input file are you using?
The error message you are getting I think results from the conjugate
gradient minimizer (I've never seen it happen for the steepest descent
minimizer). If you force more steepest descent steps, you will probably
get a better result.
HTH,
Jason
On Mon, Sep 3, 2012 at 2:13 PM, Sanjib Paul <sanjib88paul.gmail.com> wrote:
> Dear Amber Users,
> I wanted to minimize a system. But as
> soon as I run the sander, it stops. It is just after the 1st step. And
> some messages are also coming.
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 1 -7.2331E+03 1.1552E-04 3.2026E-03 NH1 2806
>
> BOND = 147.2861 ANGLE = 727.4258 DIHED =
> 2461.9612
> VDWAALS = -2220.3012 EEL = -22115.2233 HBOND =
> 0.0000
> 1-4 VDW = 857.2598 1-4 EEL = 12908.4987 RESTRAINT =
> 0.0000
>
> .... RESTARTED DUE TO LINMIN FAILURE ...
>
> .... RESTARTED DUE TO LINMIN FAILURE ...
> Frac coord min, max: 2.385924641392738E-002 1.06940190445787
> 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
>
> As here is written, if I have a restart file then the problem can be
> resolved by restarting the program,I set ntwr = -1 to get restart file
> for every step. I thought I would get the coordinates generated
> after this first step and I would restart it. But when run the program
> again with ntwr = -1, it is stopping like previous but I did not get
> any restart file. So, now how can I proceed?
>
> Sanjib
>
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>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Mon Sep 03 2012 - 15:00:03 PDT
