Hi Hosein,
Without all input files (crd, prmtop, mdin), it is hard to verify what
is really wrong. Nevertheless, it seems to me the problem could be the
definition of de/re-charge regions. Improper choices of the de/re-charge
atoms could lead to the well-known end-point problems--it seems it is the
case in your du/dl curves. One easy thing to try is change sc_beta to a
larger value (say 17) and see if there is any difference. A yes would be
strong evidence of the end-point problem.
If possible, could you post all your input files and at least one output
file, say the lambda=1 result of the de-charge step?
Thanks!
Taisung
On Mon, Feb 10, 2020 at 5:14 AM Hosein Geraili Daronkola <
geraili.hsn.gmail.com> wrote:
> Hi all,
>
> What can be possibly wrong in this, that it never works? A mutation from
> Asp to Asn with 21 lambdas, and separated to three steps of charging Asn,
> decharging Asp, and vdW. It's already equilibrated for sure. I am using the
> "alchemical_analysis" to get the result, and the O_MBAR and the TI graph
> are almost smooth and good for vdW part, but the result for the
> decharge and charge is attached and not acceptable. What did I do wrong?
>
>
>
> This is the simulation details for the decharge of Asp:
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
> *TI simulation &cntrl imin = 0, nstlim = 15000000, irest = 1, ntx = 5, dt
> = 0.001, ntt = 3, temp0 = 298.0, gamma_ln = 5.0, ig = -1, !ntc = 2, ntf
> = 1, cut=10, ntp = 1, pres0 = 1.0, taup = 2, ioutfm = 1, iwrap = 1,
> ntwe = 500, ntwx = 50000, ntpr = 500, ntwr = 500, icfe = 1, clambda =
> 0.20, scalpha = 0.5, scbeta = 12.0, logdvdl = 0, ifmbar = 1,
> mbar_states = 21, mbar_lambda = 0.00, 0.05, 0.10, 0.15, 0.20, 0.25, 0.30,
> 0.35, 0.40, 0.45, 0.50, 0.55, 0.60, 0.65, 0.70, 0.75, 0.80, 0.85, 0.90,
> 0.95, 1.00, nmropt = 1, ntr = 1, restraint_wt = 50.0,
> restraintmask='!(:WAT,K+,Cl-) & (.N,CA,C,O)', timask1 = ':34', timask2 =
> ':130', ifsc=1, scmask1=':34.CB,HB2,HB3,CG,OD1,OD2',
> scmask2=':130.CB,HB2,HB3,CG,OD1,OD2', crgmask =
> ':34.CB,HB2,HB3,CG,OD1,OD2', !method 2: !scmask1 = '', scmask2 =
> ':163.HG=' / &ewald skinnb = 5, dsum_tol = 1E-06, / &wt type = 'END' /*
>
>
>
>
> best regards
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Feb 11 2020 - 07:00:02 PST
