Dear Amber users,
I am doing TI using DDBoost and I am struggling to restart final
production H-REMD simulation, which was stopped due to job time limit.
Our cluster prefers short jobs (4 h) for its efficient utilization.
According to manual T-REMD can be restarted using -A flag instead of -O,
but amber does not recognize -A flag. I tried changing starting rst7
file in groupfile, but all output files were overwritten. I need to
append new data to existing mdout file for subsequent analysis.
groupfile:
-O -p unisc.parm7 -c t1/0.00000000_preTI.rst7 -i
inputs/0.00000000_ti.mdin -o t1/0.00000000_ti.mdout -r
t1/0.00000000_ti.rst7 -x t1/0.00000000_ti.nc -ref t1/0.00000000_preTI.rst7
-O -p unisc.parm7 -c t1/0.10000000_preTI.rst7 -i
inputs/0.10000000_ti.mdin -o t1/0.10000000_ti.mdout -r
t1/0.10000000_ti.rst7 -x t1/0.10000000_ti.nc -ref t1/0.10000000_preTI.rst7
-O -p unisc.parm7 -c t1/0.20000000_preTI.rst7 -i
inputs/0.20000000_ti.mdin -o t1/0.20000000_ti.mdout -r
t1/0.20000000_ti.rst7 -x t1/0.20000000_ti.nc -ref t1/0.20000000_preTI.rst7
-O -p unisc.parm7 -c t1/0.30000000_preTI.rst7 -i
inputs/0.30000000_ti.mdin -o t1/0.30000000_ti.mdout -r
t1/0.30000000_ti.rst7 -x t1/0.30000000_ti.nc -ref t1/0.30000000_preTI.rst7
-O -p unisc.parm7 -c t1/0.40000000_preTI.rst7 -i
inputs/0.40000000_ti.mdin -o t1/0.40000000_ti.mdout -r
t1/0.40000000_ti.rst7 -x t1/0.40000000_ti.nc -ref t1/0.40000000_preTI.rst7
-O -p unisc.parm7 -c t1/0.50000000_preTI.rst7 -i
inputs/0.50000000_ti.mdin -o t1/0.50000000_ti.mdout -r
t1/0.50000000_ti.rst7 -x t1/0.50000000_ti.nc -ref t1/0.50000000_preTI.rst7
-O -p unisc.parm7 -c t1/0.60000000_preTI.rst7 -i
inputs/0.60000000_ti.mdin -o t1/0.60000000_ti.mdout -r
t1/0.60000000_ti.rst7 -x t1/0.60000000_ti.nc -ref t1/0.60000000_preTI.rst7
-O -p unisc.parm7 -c t1/0.70000000_preTI.rst7 -i
inputs/0.70000000_ti.mdin -o t1/0.70000000_ti.mdout -r
t1/0.70000000_ti.rst7 -x t1/0.70000000_ti.nc -ref t1/0.70000000_preTI.rst7
-O -p unisc.parm7 -c t1/0.80000000_preTI.rst7 -i
inputs/0.80000000_ti.mdin -o t1/0.80000000_ti.mdout -r
t1/0.80000000_ti.rst7 -x t1/0.80000000_ti.nc -ref t1/0.80000000_preTI.rst7
-O -p unisc.parm7 -c t1/0.90000000_preTI.rst7 -i
inputs/0.90000000_ti.mdin -o t1/0.90000000_ti.mdout -r
t1/0.90000000_ti.rst7 -x t1/0.90000000_ti.nc -ref t1/0.90000000_preTI.rst7
-O -p unisc.parm7 -c t1/1.00000000_preTI.rst7 -i
inputs/1.00000000_ti.mdin -o t1/1.00000000_ti.mdout -r
t1/1.00000000_ti.rst7 -x t1/1.00000000_ti.nc -ref t1/1.00000000_preTI.rst7
mdin:
&cntrl
imin = 0
nstlim = 20
numexchg = 100000
dt = 0.001
irest = 1
ntx = 5
ntxo = 1
ntc = 2
ntf = 1
ntwx = 0
ntwr = 5000
ntpr = 1000
cut = 10
iwrap = 1
ntb = 2
temp0 = 298.
ntt = 3
gamma_ln = 2.
tautp = 1
ntp = 1
barostat = 2
pres0 = 1.01325
taup = 5.0
ifsc = 1
icfe = 1
ifmbar = 1
bar_intervall = 20
mbar_states = 11
mbar_lambda(1) = 0.00000000
mbar_lambda(2) = 0.10000000
mbar_lambda(3) = 0.20000000
mbar_lambda(4) = 0.30000000
mbar_lambda(5) = 0.40000000
mbar_lambda(6) = 0.50000000
mbar_lambda(7) = 0.60000000
mbar_lambda(8) = 0.70000000
mbar_lambda(9) = 0.80000000
mbar_lambda(10) = 0.90000000
mbar_lambda(11) = 1.00000000
noshakemask = '.1-149'
clambda = 0.00000000
timask1 = '.1-72'
timask2 = '.73-149'
crgmask = ""
scmask1 = '.31-32,39,71-72'
scmask2 = '.109-114,146-149'
scalpha = 0.5
scbeta = 1.0
gti_cut = 1
gti_output = 1
gti_add_sc = 5
gti_scale_beta = 1
gti_cut_sc_on = 8
gti_cut_sc_off = 10
gti_lam_sch = 1
gti_ele_sc = 1
gti_vdw_sc = 1
gti_cut_sc = 2
gti_ele_exp = 2
gti_vdw_exp = 2
gremd_acyc = 1
/
&ewald
/
Can you please suggest some solution?
Juraj
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Received on Tue Oct 10 2023 - 00:30:03 PDT
