From: snoze pa (snoze.pa_at_gmail.com)
Date: Mon May 05 2008 - 16:49:43 CDT
Dear NAMD users,
(sorry jim for previous mail. A pdf file was attached in previous mail.)
I did a small simulation using namd. A rmsd plot is also attached in
this mail. I am little bit confused from the figure. As shown in the
figure that the first 50ps of minimization it is working fine.
Now in equilibration, another 100ps is working fine with the lengevin
piston off.
After that i am using the "fixedatom off" and minimize for 100 ps. In
this case there is a sharp fall in rmsd as can be seen from the
figure after 150ps step(50ps of minimization+100ps of minimization
with lengevin piston off). Again after that it goes smoothly with
step wise heating and finally full MD run till 2ns.
Why the rmsd drop sharply at 151ps when "fixedatom off" is used. Am i
doing alright or there is some problem.
I am using the equilibration step taken from
http://www.ks.uiuc.edu/Research/namd/tutorial/NCSA2002/hands-on/09_equil.html
the namd.jpg file can be accessed via
http://img519.imageshack.us/img519/9688/namdtx1.jpg
Thank you very much for your help.
s
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