I don't have any suggestion for your specific problem, but it might help to
say more about these steps. when you say "charge, vdw, decharge" it might
be sensitive to which transformation you are doing. Normally if you are
disappearing an atom you would start with a decharge, then change vdw, then
add charges to the new atom. Doing that by charging the new atom without
having vdw there would cause problems, as would removing a vdw before doing
the decharge step. So I'm not sure if people will be able to help without
knowing what your system looks like at the endpoints.
On Thu, Dec 12, 2019 at 10:22 AM Hosein Geraili Daronkola <
geraili.hsn.gmail.com> wrote:
> Hi,
>
> I am using AMBER18, for mutating ASP to ASN, using 21 lambda, in three
> steps of charge, VDW, decharge. The VDW works fine, but for the charge and
> decharge step I encounter the following problem:
>
>
>
>
> difficulty in handling lambda = 1.0
>
> simulations fail for lambda = 1.0, even though there is no problem up to
> 0.95.
>
> What usually happens is density significantly drops down during the
> simulation at constant pressure.
> Making the time step interval shorter did not help.
>
> I just wonder why this happens at lambda = 1.0, though
> it does not happen at lambda = 0.0.
> (States at lambda = 0.0 and 1.0 are more or less symmetric.)
>
> Is there any suggestion to avoid this problem?
>
>
>
>
> *This is my simulation input:*
>
>
> &cntrl
> imin = 0, nstlim = 1000000, 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 = 2.0,
> ioutfm = 1, iwrap = 1,
> ntwe = 500, ntwx = 50000, ntpr = 500, ntwr = 500,
>
> icfe = 1, clambda = %L%, scalpha = 0.5, scbeta = 12.0,
> logdvdl = 0,
> ifmbar = 1, mbar_states = 21,
> mbar_lambda = %L1%,
>
> nmropt = 1,
> ntr = 1, restraint_wt = 30.0,
> restraintmask='!(:WAT,K+,Cl-) & (.N,CA,C,O)',
>
> timask1 = ':34', timask2 = ':130',
> ifsc = 0, crgmask = ':34',
>
> /
>
>
> &ewald
> skinnb = 5,
> dsum_tol = 1E-06,
> /
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>
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Received on Thu Dec 12 2019 - 10:00:02 PST
