AMBER Archive (2009)

Subject: Re: [AMBER] High RMSD for DNA: A to B transition study

From: David A. Case (case_at_biomaps.rutgers.edu)
Date: Fri Mar 06 2009 - 08:57:02 CST

On Fri, Mar 06, 2009, BERGY wrote:

>
> I am doing a Simulation of ADNA (12mer) for 10ns using AMBER9. On
> analyzing, i find that the RMSD goes well above 20-30 Angstroms. And
> visualization I see that 3 of the Bases got flipped out from the
> middle of the helix and the helix looks very much straightened like
> a ladder.

Presumably, everything up to the "production" step was fine, since you
had strong restraints to the starting structures. But you should check
this.

> --------------production---10ns---in 10ps steps
> ADNA-md1 12mer solvent-+ randomized ions
> &cntrl
> imin = 0, irest = 1, ntx = 7,
> ntb = 2, pres0 = 1.0, ntp = 1,
> taup = 2.0,
> cut = 10,
> ntc = 2, ntf = 2,
> tempi = 300.0, temp0 = 300.0,
> ntt = 3, gamma_ln = 1.0,
> nstlim = 5000, dt = 0.002,iwrap=1
> ntpr = 100, ntwx = 100, ntwr = 1000
> /

First, check to see *when* the DNA fell apart -- was it in the first 10
ps? You may have a bad structure or bad contacts. Then jumping
directly from very strong constraints (force constant of 25) to none
could cause bad behavior right away.

Alternatively, you are hitting the random number problem with ntt=3: you
are running many very short runs, then restarting with the same random
number seed over and over again. This could really explain the behavior
you see, if nothing else is wrong. You *must* use a new value of ig at
each restart...see the mailing archives for a discussion of this point.
(It's not clear why you are running 1000 separate short simulations
anyway.)

...hope this helps...dac

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