tangxuan wrote:
Hi Mark,
Thanks very much for your reply. I checked the structure of A and B at
these three ps, and there is no much change in the structures. Then I
calculated the reside area in A+B at these three specific time
(1536,15937,15938), and it shows that there are a big diffrence in size
of area at many resides between three ps. Maybe the big changes of total
SAS in interaction region at 15938 ps is because of big size of two
subunits(each has 471 resides). What is your idea?
Tang, this is most likely all due to periodic boundary conditions.
Please run
trjconv -pbc mol -ur compact on your trajectory.
Thanks,
Tang jiaowei
On Wed, 2007-10-31 at 01:59 +1100, Mark Abraham wrote:
tangxuan wrote:
Yes, the default value of -pbc is 'yes'. I did not add it in my command,
but i think pbc should has been considered. It seems there is no
contact between the two subunits, but at some specific time the total
ASA of interaction region is very high(shown below).
time total SAS of interaction region
15936 1.16099999999997
15937 1.09100000000004
15938 86.954
Have a look at your trajectory to see what the structures are doing here.
Mark
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________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
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