Dear all,
I fixed my above problem by doing an energy minimization, and the program could run and finish. But in the decharge step, the heat.out file and ti001.out file have the mbar energies from different lambda values being exactly the same as shown below:
MBAR Energy analysis:
Energy at 0.0000 = -14117.120638
Energy at 0.1000 = -14117.120638
Energy at 0.2000 = -14117.120638
Energy at 0.3000 = -14117.120638
Energy at 0.4000 = -14117.120638
Energy at 0.5000 = -14117.120638
Energy at 0.6000 = -14117.120638
Energy at 0.7000 = -14117.120638
Energy at 0.8000 = -14117.120638
Energy at 0.9000 = -14117.120638
Energy at 1.0000 = -14117.120638
Although at different runs, the energy data were different. Then in the summary, the dvdl values over 10000 steps are all 0.0000 or -0.0000.
I am wondering where could be wrong in my simulations. Thank you very much.
LZ
________________________________
From: laura zhang via AMBER <amber.ambermd.org>
Sent: Sunday, August 21, 2022 8:10
To: amber.ambermd.org <amber.ambermd.org>
Subject: [AMBER] one question about setting up scmask and timask
Dear Amber users,
I work on the relative binding free energy calculation using TI of Amber20. I set up the structures of two ligands with as much overlapping of their structures and coordinates as possible, then build the lib files, and frcmod files. When I overlapped those two ligands, they are only different in atoms 34, 42, and 59-64 with the pse file attached. The extra 8 atoms formed two methyl groups and they are physically faraway. In the decharge/ directory, I have the heat.in file as shown below.
heating
&cntrl
imin = 0, nstlim = 10000, irest = 0, ntx = 1, dt = 0.002,
ntt = 1, temp0 = 300.0, tempi = 50.0, tautp = 1.0,
ntc = 2, ntf = 1,
ntb = 1,
ioutfm = 1, iwrap = 1,
ntwe = 1000, ntwx = 1000, ntpr = 1000, ntwr = 5000,
nmropt = 1,
ntr = 1, restraint_wt = 5.00,
restraintmask='!:WAT & !.H=',
icfe = 1, clambda = 0.0, scalpha = 0.5, scbeta = 12.0,
logdvdl = 0,
timask1 = ':1', timask2 = ':2',
ifsc = 0, crgmask = ':2.34,42,59-64',
/
&ewald
/
&wt
type='TEMP0',
istep1 = 0, istep2 = 8000,
value1 = 50.0, value2 = 300.0
/
&wt type = 'END'
/
But I got error message when I ran it:
vlimit exceeded for step 0; vmax = 73.7945
vlimit exceeded for step 1; vmax = 34.6085
vlimit exceeded for step 3; vmax = 31.1985
Coordinate resetting cannot be accomplished,
deviation is too large
iter_cnt, my_bond_idx, i and j are : 4 2 38 10
I am wondering where is wrong and how to fix it. Thank you very much.
LZ
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Received on Mon Aug 22 2022 - 12:30:03 PDT
