DNA out of a box

From: Xiaolin Chuang <xiaolin_chuang_at_hotmail.com>
Date: Sat 17 Mar 2001 13:08:56 -0000

Dear AMBERs,

I have a big problem (for me). I have run MD of DNA(10pair). After running
production (100 ps), I found that one strand of DNA was out of the box (in
input file I set iwrap=0). My questions are;

1. I used 'ptraj' with trajectory file to bring the molecule back togetter
(in amber manual, this is use for visualization, no effect of energy). But I
found that the RMSd of original trajectory differed from RMSd of the new
trajectory obtaining from 'ptraj program'. Moreover, I tried to calculate
energy of each snapshot and I obtained the difference results from original
and new trajectories. WHY?

2. How to setup input file to aviod separating of two strands? or do you
have any suggestion?

3. In input file if I set 'iwrap=1', I know that the coordinates will be
wrapped into the box. But I don't know what is the disadvantage of running
MD, e.g. time or energy, for setting iwrap=1?

4. If I set nstlim=2 and iwrap=1, what does sander use coordinates for
running step 2, wrapped coord. or unwrapped coord.?


Thank you very much for reading my long questions and for your respondence.

Thank you,
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Received on Sat Mar 17 2001 - 05:08:56 PST
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