On Sun, Nov 30, 2014, pradeep pant wrote:
> Is the script below is fine for running a simple 100ps long minimization.
>
> &cntrl
> imin = 1,
> maxcyc = 500,
> dt = 0.02,
> nstlim = 5000,
> ncyc = 250,
> ntb = 0,
> igb = 0,
> cut = 12
> /
Following up on what Carlos said: even if you set imin=0 (in order to run MD),
you should never set dt to such a large value: keep it at 0.001 ps, unless you
set SHAKE, in which case using 0.002 should be fine.
You are asking for a vacuum calculation (ntb=0, igb=0). The Amber force
fields are not designed for this sort of calculation, and the program itself
is not optimal for this. If you really want to carry out a vaccum simulation,
(which is not recommended in general), it is usually better to set igb=6.
Using a cutoff is generally problematic for vacuum simulations. If you are
just looking for qualitative behavior, a value of 12 may be OK.
....dac
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Received on Sun Nov 30 2014 - 13:00:02 PST
