Hi everyone,
I'm wondering that is aMD suitable for simulating the flip from DFG-in to DFG-out in kinase.
Because during my 500 ns aMD simulation, the DFG domain was quite stable.
My input file is like
&cntrl
imin = 0,
irest = 1, ntx = 5,
ntb = 1, ntp = 0,
cut = 10.0,
ntr = 0,
iwrap = 1,
ntc = 2, ntf = 2, ig=-1,
tempi = 300.0, temp0 = 300.0,
ntt= 3, gamma_ln= 2.0,
nstlim= 5000000, dt= 0.002,
iamd = 3,
ethreshd = 4442, alphad = 216.8,
ethreshp = -132272, alphap = 7345,
ntpr= 2000, ntwx= 2000, ntwr= 20000
ioutfm = 1,
/
If aMD was suitable, could someone give me some suggestion?
Another question is it reasonable to study DFG-flip using conventional MD with simulation temperature at 1000K ? Since I have read paper did so.
Thank you all in advance.
Best wishes
Shushu
--
Shushu Zhang
Post-Doc. of CADD & Medicinal Chemistry
Research Center for Drug Discovery
School of Pharmaceutical Sciences, Sun Yat-Sen University
132 East Circle at University City, Guangzhou, China 10006
Web: www.RCDD.org.cn
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Received on Fri Nov 10 2017 - 08:00:03 PST
