Hello,
You should, in my opinion, always use ntx=5 if your restart file has
velocities from a previous simulation. (ntx=7 is not terribly well
documented in the manuals I have, and ntx=5 reads in formatted coordinates,
velocities, and box dimensions if ntb>0, which is what you're trying to do
as far as I can tell).
Furthermore, be aware of the well-documented limitations of using ff99. I
believe it is generally suggested that ff99 be avoided in favor of the far
more recent (and accurate) ff99SB force field. The SB modifications fix the
backbone torsions that tend to over-stabilize alpha-helices, if I recall
correctly.
In any case, unless you have a specific reason for choosing ff99, I would
suggest ff99SB or something newer.
All the best,
Jason
On Fri, Jun 4, 2010 at 2:05 PM, ashutosh shandilya <izerokelvin.gmail.com>wrote:
> 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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--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Fri Jun 04 2010 - 11:30:05 PDT
