Dear Amber Community,
My minimization for a lambda window in TI is behaving oddly. The energy first decreases from 6.1363E+06 to 1.5983E+06 and then increases to 1.6415E+06 over 10000 steps. Below is my input. timak and scmask define the enter residue being mutated. The troubling result is the same if I restrict the softcore region to only the appearing /disappearing atoms. What am I doing wrong?
minimisation
&cntrl
imin = 1, ! minimization on
ntmin = 2, ! Only the steepest descent method is used
maxcyc = 10000, ! The maximum number of cycles of minimization
ncyc = 5000, ! minimization will be switched from steepest descent to conjugate gradient
ntpr = 1000, ! Print the progress of the minimization every ntpr steps
ntwe = 1000, ! Every ntwe steps, the energies and temperatures will be written
dx0 = 1.0D-7, !The initial step length. If the initial step length is too big then will give a huge energy
ntb = 1, !Constant volume periodic boundaries
cut = 12.0,
!nmropt = 1,
ntr = 1, restraint_wt = 100.00,
restraintmask='!:WAT',
icfe = 1, !free energy calculations
ifsc = 1, !1 SC potentials are used
clambda = 0.50, !Zero corresponds to the unperturbed Hamiltonian V0. l=1 corresponds to the perturbed Hamiltonian V1
scalpha = 0.5, ! default value is 0.5
scbeta = 12.0, ! Default value is 12A2
logdvdl = 0, !If set to .ne. 0,calculated during every step of the run will be printed out at the end of the simulation
klambda = 1, !
timask1='.3630,3631,3632,3633,3634,3635,3636,3637,3638,3639,3640,3641,3642,3643,3644,8025,8026,8027,8028,8029,8030,8031,8032,8033,8034,8035,8036,8037,8038,8039,8040,8041,8042,8043,8044,8045,8046',
timask2='.8791,8792,8793,8794,8795,8796,8797,8798,8799,8800,8801,8802,8803,8804,8805,8806,8807,8808,8809,8810,8811,8812,8813,8814,8815,8816,8817,8818,8819,8820,8821,8822,8823,8824,8825,8826,8827’,
scmask1='.3642,3643,3644,8037,8038,8039,8040,8041,8042,8043,8044,8045,8046',
scmask2='.8803,8804,8805,8806,8807,8808,8809,8810,8811,8812,8825,8826,8827',
/
&ewald
/
&wt type = 'END'
/
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Received on Thu Sep 01 2022 - 20:30:03 PDT
