Dear amber experts,
I'm trying to compute the aboslute binding free energy with thermodynamic intergration method. The following paramters are for the GPU runing of AMBER20. In actually, I copied them from other colleague. However, I can’t judge whether these parameters are appropriate. The ':1', parmater represent the transforming ligand. Until now, these parameters still work no badly. Please help me to optimize the paramters, or correct my mistakes. Thanks in advance!
imin = 0, nstlim = 1000000, irest = 1, ntx = 5, ntxo = 1,dt = 0.001, ntb = 2, ntt = 3, temp0 = 300, gamma_ln = 5.0, ig = -1,
ntp = 1, barostat = 2, mcbarint = 100, pres0 = 1, taup = 2.0, ioutfm = 1, iwrap = 0, ntwe = 1000, ntwx = 1000, ntpr = 1000, ntwr = 1000,
cut = 10.0, ntc = 2, ntf = 1, noshakemask = ':1', icfe = 1, ifsc = 1, gti_add_sc = 2, clambda = 1.0, ifmbar = 1, bar_intervall = 1,mbar_states = 11, mbar_lambda = 0.0 0.1 0.2 0.3 0.4 0.5 0.6 0.7 0.8 0.9 1.0 , timask1 = ':1', timask2 = '', scmask1 = ':1', scmask2 = '', vlimit = 20
Best regards,
--------------------------------
Ning Wang <PhD>
National Laboratory of Biomacromolecules
Institute of Biophysics, Chinese Academy of Sciences
My reseached interests has foucsed on protein structure determinated by Cryo-EM, virtual screening of potential drugs, protein molecular dynamic simulation, and protein design via computational biology.
ORCID:
https://orcid.org/0000-0002-5019-2747
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Received on Mon Aug 30 2021 - 21:00:02 PDT
