> I haven't run the production run i have only equilibrated after heating.2ns
> MD. My input file is
>
> equilibration on protein
> &cntrl
> imin = 0,
> irest = 0,
> ntx = 1,
You are throwing away all your velocities.. (irest=0, ntx=1)
> ntb = 1,
> cut = 10,
> ntc = 2,
> ntf = 2,
> tempi = 300.0,
> temp0 = 300.0,
...and forcing it to 300K.
No wonder you are losing structure.
If everything is warmed, try ntx=5, irest=1.
If not warmed, it should be warmed gradually and/or with restraints
on your solute.
> ntt = 3,
> gamma_ln = 1.0,
> nstlim = 2000000, dt = 0.001,
> ntpr = 200, ntwx = 500, ntwr = 1000
> /
> I may switch to constant volume but what difference it would make .
It would be less fluctuation affecting the coordinates. Subtle,
but might make a difference if you had a sensitive structure. Some
believe in this method for general production runs.
It's not so important compared to the issue above.
Bill
> I have
> heated at constant volume.
> yes I have plotted the graph between density it is constant.
> Thanks and regards
> Ashutosh Shandilya
> On 4 June 2010 22:52, Bill Ross <ross.cgl.ucsf.edu> wrote:
> > > In context of my previous mail the helix is getting unfolded and
> > sometimes
> > > sheets are disappearing as well because of 2.1ns md simulation in water
> > at
> > > constant pressure.Which structure shall I take and the reason for
> > unfolding.
> >
> > It would help to send your production mdin.
> > Also your equilibration mdin's to see how well-equilibrated things are.
> > Did you graph the energy and density to be sure they were equilibrated?
> >
> > Your homology model might be wrong, but it could also be your
> > equilibration. One thing that would be interesting to try would
> > be to switch to constant volume once density is correct.
> >
> > Bill
> >
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Received on Fri Jun 04 2010 - 11:00:07 PDT
