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
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> 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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Received on Mon Jul 04 2011 - 00:00:03 PDT
