Dear List,
I am trying to do some test runs with dual boost in GaMD (AMBER 16 version).
I read PNAS and JCTC papers where several short simulations with no boost
potential were carried out to identify the optimal σ0 and *k*0 acceleration
parameters.
I am trying to do the same and below is my input file for GaMD test run.
However, I am not able to figure out from output file the maximum, minimum,
average and standard deviation values of the system potential. I tried to
vary the sigma0P and sigma0D. My apologies for ignorance, could you please
point me how can I do perform test runs in AMBER 16 to calculate the
optimal sigma0 and k0 parameters? Do I need to change igamd =1?
&cntrl
imin = 0, irest = 0, ntx = 1,
nstlim = 5000000, dt = 0.002,
ntc = 2, ntf = 2, tol = 0.000001,
iwrap = 1, ntb = 1, cut = 10.0,
ntt = 3, temp0 = 298.0, tempi = 298.0,
ntpr = 1000, ntwx = 1000, ntwr = 1000, gamma_ln=3.0,
ioutfm=1,iwrap=1,ig=-1,
igamd = 0, iE = 1, irest_gamd = 0,
ntcmd = 1000000, nteb = 1000000, ntave = 50000,
sigma0P = 6.0, sigma0D = 6.0,
&end
Thank you for your attention and consideration in advance.
Cheers,
Neha
--
Regards,
Dr. Neha S. Gandhi,
Vice Chancellor's Research Fellow,
Queensland University of Technology,
2 George Street, Brisbane, QLD 4000
Australia
LinkedIn
Research Gate
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Aug 01 2017 - 16:30:02 PDT
