Hello Mr Jason & Mr. Dac,
Yes it is conjugate gradient
minimization. Before this minimization I minimized this system for
110000 steps. At first for 15000 steps where I used the following
input file-
minimization
&cntrl
imin = 1,
ntb = 0,
igb = 0,
ncyc = 2500,
maxcyc = 15000,
cut = 99
/
After this I minimized the system for two times using the following input file.
minimization
&cntrl
imin = 1,
ntb = 0,
igb = 0,
ntmin = 0,
maxcyc = 50000,
drms = 0.000001,
cut = 99
/
Now when I am going to minimize it for third time the errors which I
posted before are coming.
So, should I use igb = 6?
Sanjib
On Tue, Sep 4, 2012 at 6:14 AM, case <case.biomaps.rutgers.edu> wrote:
>
> 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
>
>
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Received on Tue Sep 04 2012 - 08:00:04 PDT
