Dear Amber users,
I am trying to simulate protein model. I minimized the system and then slowyl with restraints on
the bacbone atoms I heated up now I would like to do the equilibration step.
I made this input file.
pressure equilibration
&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 = 300.0, temp0 = 300.0,
ntt = 3, gamma_ln = 1.0,
nstlim = 250000, dt = 0.002,
ntpr = 200, ntwx = 200, ntwr = 200
>>>restraintmask=':1-255.CA,C,N', restraint_wt=,
I dont have much experiences, so maybe someone could tell me if this input good or maybe I
should change or add something, what about the restraints should I include it also in this step?
thank you for any help
Best Regards,
Urszula Uciechowska
MSc.PhD Student
Medicinal Chemistry Group
University of Halle-Wittenberg
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Received on Sun Dec 16 2007 - 06:07:07 PST
