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?
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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.?
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Thank you very much for reading my long questions and for your respondence.
Thank you,
Xiaolin
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Received on Sat Mar 17 2001 - 05:08:56 PST
