On Mon, Sep 03, 2012, Sanjib Paul wrote:
> 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.
As Jason said, we would need more information. Is SHAKE turned on? You
already have a system with a very low RMS gradient, and sander won't go beyond
this if SHAKE is on.
Also, it looks like you are simulating a non-periodic (aka vacuum) simulation.
It would be of interest to know how you prepared this system (given the very
low gradient). It's often better to use igb=6 for vacuum simulations -- you
won't have the problem with a virtual box.
....dac
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Sep 03 2012 - 18:00:02 PDT
