Hello Amber-Users,
I want to do an umbrella sampling for a residue in my protein, but I've
got a few question how to start this:
I've got my mdin-file:
&cntrl
imin = 0, irest = 1, ntx = 7,
ntb = 2, pres0 = 1.0, ntp = 1,
taup = 2.0,
cut = 9, ntr = 0,
ntc = 2, ntf = 2,
tempi = 298.15, temp0 = 298.15,
ntt = 3, gamma_ln = 1.0,
nstlim = 250000, dt = 0.002,
ntpr = 200, ntwx = 200, ntwr = 200
/
&wt type='DUMPFREQ', istepl=10 /
&wt type='END' /
DISANG=chi.RST
DUMPAVE=chi_vs_t.170
and the chi.RST-file:
&rst iat=9,10,11,12,13,14, r1=0., r2=170., r3=170., r4=360., rk2=30.,
rk3=30., /
1) Where can I find some appropriate restraints for the residue?
2) I want to separate my md in smaller parts about 500ps. So is the
DUMPAVE-file overwritten with every new start, and do I have to change
the name for every new 500ps?
Thanks for your help!
--
German Erlenkamp
Institut fuer Pharmazeutische Chemie
Martin-Luther-Universitaet Halle
Wolfgang-Langenbeck-Str.4
06120 Halle/ Saale
E-Mail: german.erlenkamp.pharmazie.uni-halle.de
Phone: (49)345 - 55 25 043
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" (in the *body* of the email)
to majordomo.scripps.edu
Received on Wed May 28 2008 - 06:07:26 PDT
