Hi, Luis
The umbrella files 01-04 are identical in multiple walker ABMD, so you can
just
take the first one to do analysis.
Feng
On Mon, Jan 25, 2021 at 4:04 PM Luis Simon <lsimon.usal.es> wrote:
> 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!
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Feng Pan
PostDoc
Florida State University
Department of Statistics
Email: fpan3.ncsu.edu; fpan.fsu.edu
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Jan 29 2021 - 13:00:02 PST
