Dear All,
I am doing Umbrella Sampling on a pair of dodecamer and I would like to
obtain the PMF as a function of the relative distance and orientation.
I have noticed that I have to use a lot of restrains.
My question is:
is it right to put the restraint for each bond? Is it right to obtain the
PMF?
My restraint files is like this:
#DNA
#dna
&rst
iat=62,820
r1=0.0000E+00,r2=28.0000,r3=28.0000,r4=56.000,rk2=5,rk3=5,ir6=0,
&end
&rst
iat=92,850
r1=0.0000E+00,r2=28.0000,r3=28.0000,r4=56.000,rk2=5,rk3=5,ir6=0,
&end
&rst
iat=125,883
r1=0.0000E+00,r2=28.0000,r3=28.0000,r4=56.000,rk2=5,rk3=5,ir6=0,
&end
......
thank you in advance
Elisa
--
Elisa Frezza
Ph.D. Student in Materials Science and Engineering
Dipartimento di Scienze Chimiche
Università di Padova
via Marzolo, 1
35131 Padova - Italy
Phone: +39 049 827 5149
Skype: elisa.frezza
Emai: elisa.frezza.gmail.com
elisa.frezza.studenti.unipd.it
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Received on Tue Jan 15 2013 - 06:30:02 PST
