Thanks for quick reply
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,
ntb = 1,
cut = 10,
ntc = 2,
ntf = 2,
tempi = 300.0,
temp0 = 300.0,
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 .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 - 11:00:05 PDT
