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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Received on Thu Dec 12 2019 - 07:30:02 PST
