2015-08-18 4:58 GMT-06:00 Rom <[email protected]>: > 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? 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 > > -- > You received this message because you are subscribed to the Google Groups > "votca" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to [email protected]. > To post to this group, send email to [email protected]. > Visit this group at http://groups.google.com/group/votca. > For more options, visit https://groups.google.com/d/optout. -- Christoph Junghans Web: http://www.compphys.de -- You received this message because you are subscribed to the Google Groups "votca" group. To unsubscribe from this group and stop receiving emails from it, send an email to [email protected]. To post to this group, send email to [email protected]. Visit this group at http://groups.google.com/group/votca. For more options, visit https://groups.google.com/d/optout.
