I have slowly heated the protein and water each step of 5Kelvin and i have
used irest=1 and ntx=7 for 60 steps for 2.5ps each for 5 Kelvin till 300K.
2.5ps MD equilibration on protein
&cntrl
imin = 0,
irest = 1,
ntx = 7,
ntb=2,
ntp = 1,
taup=2.0,
pres0 =1.0
cut = 10,
ntc = 2,
ntf = 2,
tempi = 20.0,
temp0 = 25.0,
ntt = 3,
gamma_ln = 1.0,
nstlim = 2500, dt = 0.001,
ntpr = 200, ntwx = 500, ntwr = 1000
/
Shall i use irest=1 ntx=7 during equilibration too.
Thanks and regards
Ashutosh Shandilya
On 4 June 2010 23:26, Bill Ross <ross.cgl.ucsf.edu> wrote:
> > 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 - 11:30:03 PDT
