Dear Amber Users and Developers
I am trying to perform a QMMM SMD simulation to monitor a PT reaction.
I equilibrated my system and obtained replicates, However when I subject
the replicates to SMD using the fallowing parameters and sander.MPI, it
seems like sander is not reading the ncsu section and the variables. When I
repeat the exact same simulation with Amber 14, from output file I can see
that the SMD is going to be performed. I even run the input files from the
SMD AMBER tutorial using both Amber16 and Amber14 and still the same, Amber
16 does not read the ncsu section. Has there been any modification
regarding these parameters on Amber16, I couldn't find anything different
in Amber16 manual.
here are my input parameters:
LYS12H2O: PT using NCSU steered MD with LCOD rxn coord
&cntrl
imin = 0,
irest = 0,
ntx = 1,
ntb = 0,
cut = 999.0,
tempi = 300.0,
temp0 = 300.0,
ntt = 3,
gamma_ln = 1.0,
ntf = 2, ntc = 2, tol = 0.00001, nscm = 0,
dt = 0.0005,
ntpr = 100, ntwr=100, ntwx = 100,
nstlim = 100000,
ifqnt = 1,
/
&qmmm
qmmask=':12, 23 ', !QM region mask LYS 12 and a SINGLE WATER
qmcharge=1, !QM region charge, not total system
qm_theory='DFTB',
qmshake=0,
writepdb=1,
/
ncsu_smd
output_file = 'SMD_200.dat'
output_freq = 1000
variable
type = LCOD ! Linear Combination of Distance
i = (139,140,270,140)
r = (1.0,-1.0)
path = (3.3461,-3.3461)
harm = (1000.0)
end variable
end ncsu_smd
Best Regards,
Sam
--
*Samaneh ghassabi kondalaji*
*PhD student in Chemistry*
*555 CRL, Chemistry department*
*West Virginia University *
*Morgantown, USA*
*E-mail: **saghassabikondalaji.mix.wvu.edu*
<saghassabikondalaji.mix.wvu.edu>
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Received on Thu Apr 13 2017 - 09:00:02 PDT
