Angle files (conversion issues)

[Rom]

Hi guys,

What seems simple seems to be causing alot of issues with my system being able to run. Theres a few issues, so I'll list them as they have appeared: (please note, before running, I convert my file names to the required 'table_a1.xvg' etc)


(1) I have my angle file in radians, and need to convert to degrees. What I do is run a simple awk script to convert, but both give me issues


awk -v scale='180/3.1415' '/^[^@#]/{print $1*scale,$2,$3}' < angle_str_1_new.xvg > angle_str_1_new2.xvg

This appears to take my radians scale (0 to pi), and yet the degrees come out as 0 - 500 (needs to be within 0 and 180).


awk '{print $1*57.2957795,$2,$3}' < angle_str_1_new.xvg > angle_str_1_new2.xvg

so I ran this simpler command, and it gives me the main curve within 0 and 180 degrees, which is great, however, when I then attempt my mdrun, it spits out an error of the X values (the degree column), not being equally spaced, and I'm not sure how to stop this when converting over from radians (or if anyone else got around this issue?)



(2) For the second awk script above, which gave me the potential within the correct range, I then edited the file to be only with 0 and 180 (simply deleting anything over 180), and i get the following error(s) when attempting to run:

Having edited the file to go from only 0 to 180, with the very last line of my file having exactly '180', I get an error saying the values should go from 0 to 180, not 0 to 179.998 (even though my file goes to 180?)


I then edited the file to include some values in the higher 180.XXX range, and then get the error: 

The angles in file table_a1.xvg should go from 0.000000 to 180.000000 instead of 0.000000 to 0.000000


So I think I may be doing something incorrect on a very simple task! Anyone else have these issues above, and no how to solve it?

[Christoph Junghans]

The problem in (1) is that awk interprets '180/3.1415' as string,
which value is something like 180 (see awk '{print 1.*"180/3.1415"}')
and hence it goes up to 560.
For (2), this is more a gromacs problem, but you could run
csg_resample on the final table to put in on the right grid:
csg_resample --in angle_str_1_new2.xvg --out angle_str_1_new3.xvg
--grid 0:0.001:180

If you have VOTCA 1.3-dev you could run:
csg_call --options settings.xml --ia-name angle --ia-type angle
convert_potential gromacs angle_str_1_new.xvg angle_str_2_new.xvg
(with settings.xml from the hexane/ibi_bonded example)
which should do the same as (2).

Christoph


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--
Christoph Junghans
Web: http://www.compphys.de