Re: [AMBER] TI on pmemd CUDA, AMBER18

From: Taisung Lee <accuratefreeenergy.gmail.com>
Date: Tue, 11 Feb 2020 09:39:33 -0500

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?
>
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> This is the simulation details for the decharge of Asp:
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> *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' /*
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> best regards
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>
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Received on Tue Feb 11 2020 - 07:00:02 PST
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