[AMBER] DNA simulation

From: najmul arfin <syednajmularfin.gmail.com>
Date: Sun, 3 Jul 2011 22:55:38 -0700

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
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-- 
NAJMUL ARFIN
Research  Scholar
SCHOOL OF PHYSICAL SCIENCES,
JAWAHARLAL NEHRU UNIVERSITY,
NEW DELHI -110067
+919910040525







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Received on Sun Jul 03 2011 - 23:00:05 PDT
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