Hi Amber community,
I have been trying to run some TI simulations on peptide side-chain mutations and although they run fine normally and I can get dV/dl I would ideally like to use MBAR to calculate my free energy changes.
However, when I add the MBAR options from the manual to the end of my input file all I get back is the error in reading namelist control.
Here are the options that I am specifying in my input file:
imin = 0, nstlim = 2500000, irest = 1, ntx = 5, dt = 0.002,
ntt = 3, temp0 = 298.0, gamma_ln = 2.0, ig = -1,
ntc = 2, ntf = 1,
ntb = 2,
ntp = 1, pres0 = 1.0, taup = 2.0,
ioutfm = 1, iwrap = 1,
ntwe = 1000, ntwx = 1000, ntpr = 10000, ntwr = 20000, ntave = 50000,
icfe = 1, ifsc = 1, clambda = %L%, scalpha = 0.5, scbeta = 12.0,
logdvdl = 1,
scmask = ':211',
ifmbar = 1,
mbar_states = 15,
mbar_lambda = 0.01, 0.05, 0.10, 0.15, 0.20, 0.30, 0.40, 0.50, 0.60, 0.70, 0.80, 0.85, 0.90, 0.95, 0.99,
/
&ewald
/
Any help in identifying which of these settings are wrong/what I need to add to get this to work would be greatly appreciated.
Thanks,
Charlie
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Received on Fri Oct 18 2024 - 08:30:02 PDT
