Hello Amber users,
I'm running ABMD with NFE toolkit in pmemd. Here are one of the mdin files and the cv file:
Input file for abmd
&cntrl
imin=0,
ntx=1,
irest=0,
ntxo=1,
ntc=2,
ntf=2,
nstlim=19090000,
ntt=3,
gamma_ln=2.0,
tempi=300.0,
temp0=300.0,
ntpr=5000,
ntwr=5000,
ntwx=5000,
dt=0.002,
ig=-1,
ntb=1,
ntr=0,
cut=10.0,
ioutfm=1,
iwrap=1,
infe=1,
&end
&abmd
mode='FLOODING'
monitor_file='abmd_1.dat'
monitor_freq=1000
cv_file='cv.in'
timescale=10.0
umbrella_file = 'umbrella_1.nc'
wt_temperature = 10000.0
wt_umbrella_file = 'wt_umbrella_1.nc'
/
cv file:
&colvar
cv_type = 'TORSION'
cv_ni = 4
cv_i = 5653, 5639, 5620, 5551
cv_min = -3.141593
cv_max = 3.141593
resolution = 0.1
/
&colvar
cv_type = 'TORSION'
cv_ni = 4
cv_i = 5641, 5649, 5653, 3386
cv_min = -0.4
cv_max = 2.1
resolution = 0.05
/
After processing the wt_umbrella_1.nc file with nfe-umbrella-slice, the cv values and free energy are dumped to FE.dat. I found that the free energy values in FE.dat didn't change with time. Is this reasonable? Or is there something wrong with my input files and structures?
By the way, the cv_min and cv_max in the cv.in file don't seem to work, because the both the CVs change from -3.141593 to 3.141593. Could you please have a look? Thank you.
Best,
Yao Li
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Received on Thu Mar 21 2019 - 09:00:02 PDT
