Dear Najmul,
As Jason pointed out, minimizing DNA is incredbly tricky, and due to the
charges, if you don't do it properly, the double strands keep moving apart
untill it denaturates.
So, following Jason comments, I suggest you to read a paper where a dna guru
explains a kind of "standard protocol" to properly perform the
minimization/equilibration.
J. Am. Chem. Soc. 1997, 119, 7463-7469
These 3 guys are among the strongest ones on DNA simulations nowadays. On
page 7464 you can see ref. 17 (actually a footnote), where they explain the
protocol. It's the least you have to do, and I even suggest you to go beyond
it, as you have two solvents on your system.
Regards,
On Mon, Jul 4, 2011 at 3:30 AM, Jason Swails <jason.swails.gmail.com> wrote:
> Hello,
>
> I have a couple comments here: First, you are relaxing the system while
> constraining the DNA (I'm guessing that's the residues you chose) for only
> 2
> ns. Is that the same protocol that was used in the paper you're trying to
> reproduce?
>
> >From what I've heard, the equilibration needs to be careful so that the
> solvent adapts an acceptable configuration before you release the DNA to
> move around at will. Also, make sure that the solvent box is large enough
> -- I think nucleic acid simulations are particularly sensitive to small
> boxes (which would make sense given the amount of charge involved with
> typical nucleic acid systems). A real DNA/RNA guru would have to chime in
> here.
>
> Lastly, the restraints that you're using for the heating process are very
> excessive in my opinion. A force constant of 500 is incredibly stiff, and
> gives rise to very high-frequency motions that require a small time step to
> properly integrate. A force constant of ~5-10 is also very stiff, will
> have
> the same effect in terms of keeping the DNA fixed, but will allow for a
> larger time step (and a more efficient solvent reorganization). Note that
> the above does not apply for a minimization.
>
> HTH,
> Jason
>
> On Sun, Jul 3, 2011 at 11:55 PM, najmul arfin <syednajmularfin.gmail.com
> >wrote:
>
> > Dear amber users,
> > i am trying to simulate DNA in a solvent box (containing 500 water
> > molecules + 1240ethanol molecules) using* AMBER9*. I have made the box
> > using
> > packmol .After that i used xleap to load all the necessary files for DNA
> > and the box *(u can see the methodology in xleap.log as attachments)*.
> Then
> > using edit command in xleap ,i opened the visualization window . After
> that
> > i selected dna molecule and dragged it into box, then i saved the
> .prmtop
> > and .inpcrd file for the entire dna+box system.
> >
> > After that i minimized the entire system *(first as mix_min1.in and then
> > as
> > **mix_min2.in )*to get the constant energy and then i equilibrated the
> > entire system*(as md1.in ) *for 1ns to get constant energy. after that i
> > ran
> > the dynamics for 3ns*(as md2.in) *,energy is constant here also .But
> when
> > i
> > checked the RMSD value it was monotonically increasing till 5 angstrom
> and
> > while visualising in VMD , DNA seems to get apart from original
> > configuration .
> >
> > My problem is that , i was trying to reproduce a paper
> > (PNAS,VOL.94,9626-9630, 1997), where RMSD is quickly saturating at
> > 2angstrom. Paper writes that it can be done in two ways:
> > *1*. equilibrate DNA in (water +ethanol ) box for long time
> > *2. or *hydreated DNA can be used and then solvate it in ethanol box.
> > *
> > *
> > I am doing the first way, but i am not able to control the RMSD ,
> actually
> > in long equilibration no time was mentioned.
> >
> > So , how much long i have to equilibrate or is there any other way out to
> > find the time for equilibriation or is there any other problem in
> > simulation for such a behavior.
> >
> > I AM ATTACHING ALL THE NECESSARY FILES I HAVE USED FOR THE SIMULATION .
> >
> > -- regards
> > NAJMUL ARFIN
> > Research Scholar
> > SCHOOL OF PHYSICAL SCIENCES,
> > JAWAHARLAL NEHRU UNIVERSITY,
> > NEW DELHI -110067
> > +919910040525
> >
> >
> >
> > --
> > NAJMUL ARFIN
> > Research Scholar
> > SCHOOL OF PHYSICAL SCIENCES,
> > JAWAHARLAL NEHRU UNIVERSITY,
> > NEW DELHI -110067
> > +919910040525
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> >
> >
> >
> > --
> > NAJMUL ARFIN
> > Research Scholar
> > SCHOOL OF PHYSICAL SCIENCES,
> > JAWAHARLAL NEHRU UNIVERSITY,
> > NEW DELHI -110067
> > +919910040525
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> >
>
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Candidate
> 352-392-4032
> _______________________________________________
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> http://lists.ambermd.org/mailman/listinfo/amber
>
--
--
Bruno Barbosa Rodrigues
PhD Student - Physics Department
Universidade Federal de Minas Gerais - UFMG
Belo Horizonte - Brazil
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Received on Wed Jul 06 2011 - 05:00:04 PDT
