On Sat, Jun 19, 2010 at 4:09 PM, Sangita Kachhap <sangita.imtech.res.in>wrote:
>
> > Hello,
> >
> > The restraints for the constant pH simulations should not be any
> different
> > than restraints for any other simulations. What I normally do is just
> > restrain the backbone atoms (CA, N, C, and O). Since you should be using
> > SHAKE anyway, there's really no point in restraining hydrogen atoms I
> > wouldn't think. I've noticed that heating and equilibration has to be
> done
>
> is heating and equlibration is required for implicit simulation ?
>
The only times that equilibration and heating can be confidently neglected,
I would argue, is when the system being considered is quite small. The more
particles your system has, the more likely it is that not
heating/equilibrating will lead to problems (since the phase space is more
complex). In my experience, this is especially true of constant pH
simulations, so I would suggest that for any modestly sized system,
heating/equilibration should be run. Note there is really never any harm in
doing this, short of wasting (small amounts of) computer time performing
these steps.
Because in tutorial for simulation of DNA in implicit condition there is
> only
> relaxing the
> molecule then molecular dynamics run at tempi = 300.0, temp0 = 300.0
>
> so should I directly run molecular dynamics at constant pH after
> minimization?
>
You should heat and equilibrate first, but allow the protonation states to
change (i.e. set ntcnstph to some value smaller than nstlim). You certainly
can't interpret any pKa data during the heating process, since Ka is
T-dependent, but it does allow for the protonation states to 'relax' as
well.
Good luck!
Jason
>
> > more carefully with constant pH simulations as opposed to other types of
> > simulations, so you should keep relatively strong restraints for heating
> (if
> > you're using ntr, use restraint_wt=5 or something to that effect). You
> can
> > then reduce these to ~1 for your equilibration (which is run AFTER
> heating,
> > it's not a part of heating).
> >
> > If one of your steps generates a cprestrt file, you should use that as
> the
> > cpin file for the next simulation. The only real differences between the
> > cprestrt and cpin will be the resstate array. All other variables will
> be
> > the same, although the formatting will look drastically different.
> >
> > The cprestrt file will hold the protonation states (resstate) for each of
> > your titratable residues that correspond to the conformation defined in
> your
> > restrt file.
> >
> > Hope this helps,
> > Jason
> >
> > On Sat, Jun 19, 2010 at 3:55 AM, Sangita Kachhap <sangita.imtech.res.in
> >wrote:
> >
> >> Hello all
> >> I am doing constant pH simulation using amber10.
> >> I have minimized it using restriant on all hydrogen and generated restrt
> >> file.
> >> Now I have to euqilibrat it with heating 0 - 300K.
> >>
> >> Should I use restraint at this time if yes then what I should consider
> for
> >> it ?
> >>
> >> Should I make restrt and cprestrt file during equilibration?
> >>
> >> As cprestrt contains protonation state definitions, final protonation
> states
> >> for restart (same format as cpin).
> >>
> >> Anybody please suggest me.
> >>
> >> With regard
> >> Sangita Kachhap
> >> JRF
> >> BIC,IMTECH
> >> CHANDIGARH
> >>
> >> _____________________________________
>
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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 Sat Jun 19 2010 - 14:30:03 PDT
