Date: Tue, 23 Aug 2011 16:53:10 -0400
Dear Amber Users
I have observed a very strange phenomenon from trajectory visualization
using VMD. I have attached the GIF format of the trajectory animations with
this email. Owing to the fact that this mailing list limits the size of the
attachment less than 1024KB, the quality of the GIF is very poor. Movies of
higher qualities are listed with the following links:
http://dl.dropbox.com/u/5951953/1.mpg
http://dl.dropbox.com/u/5951953/1.gif
Please check them out.
I am simulating a polymer solvated in the truncated octahedral box under NPT
ensemble. The Langenvin dynamics is invoked to control the temperature. The
input script is actually copied from one official tutorial listed in Amber
Website and is presented below.
polyA-polyT 10-mer: 100ps MD
&cntrl
imin = 0, irest = 1, ntx = 7,
ntb = 2, pres0 = 1.0, ntp = 1,
taup = 2.0,
cut = 10, ntr = 0,
ntc = 2, ntf = 2,
tempi = 300.0, temp0 = 300.0,
ntt = 3, gamma_ln = 1.0, ig = -1,
nstlim = 500000, dt = 0.002,
ntpr = 100, ntwx = 100, ntwr = 1000
/
The abnormal phenomenon is that the simulation box suddenly changes its
shape like twisting within very short time step intervals. In the movie
attached, just the solute part is included in order to enable the audience
to have a better view. And this kind of twist keeps happening along the
simulation.
In my opinion, the dynamics of the polymer should not be that fast. That is
why I think it is very strange. I wonder weather what I saw is artifact and
if it is could anybody tell me how to get rid of them.
Any comments or suggestions would be highly appreciated.
Thank you very much for your time.
Best Regards!
Bin
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