Re: [AMBER] Amber

From: case <>
Date: Sat, 8 Jan 2011 08:12:19 -0500

On Sat, Jan 08, 2011, Shesh Nath wrote:

> I am simulated a DNA of 4o base pair using "" and xleap.
> I am heating it from 0 to 400K in following step.
> Stage 1 heating of DNA 0 to 50K
> &cntrl
> imin=0, irest=0, ntx=1,
> nstlim=10000, dt=0.0005,
> ntc=1, ntf=1,
> ntt=1, tautp=1.0,
> tempi=0.0, temp0=50.0,
> ntpr=50, ntwx=50,
> ntb=0, igb=0,
> cut=12.
> and continuously............
> When temperature is incresing, bonds are opening but I am getting a
> problem after 200K the one strand of DNA is partially disappeared.

You don't say what you mean by "partially disappeared", or what led you to
that conclusion. Nevertheless, you should not expect any reasonable
results to arise from running a vacuum simulation of DNA at 400 K. I guess
you will get some conformation (and am pretty sure atoms won't disappear), but
I doubt that there will be any useful information there.


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Received on Sat Jan 08 2011 - 05:30:03 PST
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