Dear Amber user:
Sorry about disturbing. I am a student of ECNU and I tried to check quantum dynamical effects in a proton transfer reaction, but I met problem in LSC - IVR after sampling with PIMD.
My LSC - IVR tasks were stuck (tasks keep running without any output information). There is no error information either. The last line of output file is shown below.
--------------------------------------------------------
4. RESULTS
--------------------------------------------------------
#####################as segmentation###################################
I used amber18 and amber tools 19. My system is solved in a non-periodic water cap. Flag ilscivr = 1 and icorf_Isc = 4 was used in LSC - IVR calculations, the number in ‘LSC_rhoa.dat’ files are between 0 and 10000.
PIMD sampling input file
&cntrl
ipimd = 1, ntx = 5, irest = 1,
ntpr = 1000, ntwr = 1000, ntwx = 1000,
ntf = 2, ntc = 2, cut = 999.0,
ntb = 0, nstlim = 1500000, dt = 0.001,
temp0 = 298.0,ntt=3, gamma_ln=2.0,
nmropt = 1, ioutfm = 1,ifqnt=1,fcap=1,
ntr=1,
restraint_wt=10,
restraintmask=':1.C1',
&end
&qmmm
qmmask=':1'
qmcharge=1,
spin=1,
qm_theory='PM6'
qmshake=0,
qm_ewald=0,
qm_pme=0,
writepdb=1,
&end
LSC test input file
&cntrl
ilscivr = 1, icorf_lsc = 4,
ntx = 1, irest = 0,
ntpr = 1, ntwr = 1, ntwx = 1,
ntf = 2, ntc = 2, cut = 999.0,
ntb = 0, nstlim = 0, dt = 0.001,
temp0 = 298.0,ntt=0,
nmropt = 1, ioutfm = 1,ifqnt=1,fcap=1,
ntr=1,
restraint_wt=10,
restraintmask=':1.C1',
&end
&qmmm
qmmask=':1'
qmcharge=1,
spin=1,
qm_theory='PM6'
qmshake=0,
qm_ewald=0,
qm_pme=0,
writepdb=1,
&end
#####################as segmentation###################################
By any chance, could you please help check the problem and give some directions?
Thank you for you reading and looking for your reply.
Regards
Yuanfei Xue
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Received on Thu Feb 06 2020 - 06:00:04 PST
