Hi Amber users…
I tried to run an abmd calculation with two dihedral angles as colvars. I tried to set some limits to these angles, but amber ignores it, as well as the resolution. This is in the output file:
NFE : CV #1 periodic, 125 points, min/max = -3.141593/3.141593
NFE : CV #2 periodic, 125 points, min/max = -3.141593/3.141593
The colvar file is at follows:
&colvar
cv_type = 'TORSION'
cv_ni = 4, cv_i = 636,634,640,641
resolution = 0.2
cv_min = -1.0
cv_max = 2.1
/
&colvar
cv_type = 'TORSION'
cv_ni = 4, cv_i = 634,640,641,644
resolution = 0.2
cv_min = -4.2
cv_max = -0.5
/
And the &abmd section of the input file is something like:
&abmd
mode='FLOODING'
monitor_file='abmd.001.txt'
monitor_freq=500
cv_file='abmd_cv.in'
umbrella_file='abmd_umbrella.001.nc'
timescale=1
selection_freq = 5000
selection_constant = 0.00001
selection_epsilon = 0.0
wt_temperature = 10000
wt_umbrella_file = 'wt_umbrella.001.nc’
(I run 4 replicas, changing abmd_umbrella.001.nc and wt_umbrella.001.nc to 002, 003, and 004 files). I also wonder which of the nc files should be used with nee-umbrella-slice program. The tutorials uses wt_umbrella.001.nc, but I wonder if the results from different walkers do not need to be combined.
Thanks for your help!
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Received on Mon Jan 25 2021 - 13:30:02 PST
