On Fri, Dec 09, 2011, Urszula Uciechowska wrote:
>
> initial minimization relax all atoms
> &cntrl
> imin = 1,
> maxcyc = 1000,
> ncyc = 500,
> ntb = 1,
> cut = 9
> /
>
> Input for heating and equilibration :
>
> equilibration
> &cntrl
> ipimd = 2,
I'm almost sure you don't want to do this. If you have little or no
experience with Amber, learn classical dynamics first. Path-integral
dynamics is a *very* advanced topic.
> ntb = 2,
> ntp = 1,
Don't try to do constant pressure equilibration directly after minimization.
Equilibrate first with constant volume.
> ntx = 5,
> irest = 1,
These two lines ask the program to continue from a previous MD run. But you
don't have a previous run. Set ntx=1, irest=0.
> cut = 9,
> temp0 = 300.0,
> ntt = 4,
> nchain = 4,
Use ntt=3 instead.
> nstlim = 10, dt = 0.0002,
> ntpr = 1, ntwx = 5, ntwr = 5,
It's good to start with a small number of steps and ntpr=1. I wish we could
get everyone to do that when they are first starting. I suggest using the
default value of dt (0.001).
...good luck...dac
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Received on Fri Dec 09 2011 - 08:00:02 PST
