I am not 100% sure what you want to do! $ csg_call --options table.xml --ia-type dihedral convert_potential input.pot table.xvg will extrapolate, shift and then convert it to xvg.
$ csg_call --options table.xml convert_potential xvg --type input.pot table.xvg will only do the reformatting (and force calculation) from pot to xvg. In the latter case you will have to make sure that input.pot goes from -180 to 180, in the former that is done by the extrapolating. convert_potential xvg knows nothing about the bins size it just reads input.pot convert_potential gromacs reads cg.inverse.gromacs.table_bins and uses it as the bin size. If the input.pot already has the right grid extrapolate will not change your potential. As a side note, make sure input.pot is in degress. Christoph 2013/8/15 <[email protected]>: > What I want to do is to first resample: > > csg_resample --in 1dihedralPOT_C --out 1dihedralRES --type cubic --grid > -180:10:180 > > and then without extrapolation make a gromacs table directly with 0.05 bins. > so csg_call --options table.xml --ia-type dihedral convert_potential gromacs > 1dihedralRES table_d1.xvg does not work properly as extrapolation is done > inbetween. How to skip extrapolation which is done wrong? > > > > On Thursday, August 15, 2013 3:08:17 PM UTC+1, [email protected] wrote: >> >> I run csg_call --options table.xml convert_potential xvg --type dihedral >> 1dihedralRES table_d1.xvg >> >> with xml options as before where <table_bins>0.05</table_bins> but my >> table_d1.xvg is spaced every 10 degrees. Could you advise please? >> >> >> >> On Thursday, August 15, 2013 2:37:54 PM UTC+1, [email protected] wrote: >>> >>> in the --help option for --type dihedral is not specified and it works >>> now. >>> >>> On Thursday, August 15, 2013 2:25:03 PM UTC+1, [email protected] wrote: >>>> >>>> >>>> >>>> On Thursday, August 15, 2013 1:08:58 PM UTC+1, [email protected] wrote: >>>>> >>>>> Dear Users, >>>>> >>>>> I am trying to create gromacs table for dihedrals: >>>>> >>>>> csg_call --options table.xml --ia-type bonded convert_potential gromacs >>>>> 9dihedralRES_extr table_d9.xvg >>>>> >>>>> where table.xml >>>>> >>>>> <cg> >>>>> <inverse> >>>>> <gromacs> >>>>> <pot_max>1e4</pot_max> >>>>> <table_end>180</table_end> >>>>> <table_bins>0.05</table_bins> >>>>> </gromacs> >>>>> </inverse> >>>>> </cg> >>>>> >>>>> But the table_d9.xvg starts from 0 to 180... I wish it starts from -180 >>>>> to 180. How can I specify it? >>>>> >>>>> Steven >>>> >>>> >>>> This command resamples and extrapolates... so not needed. I just want to >>>> convert my resampled and extrapolated dihedral to gromacs xvg: >>>> >>>> csg_call convert_potential xvg 19dihedralRES table_d19.xvg --type bond >>>> >>>> ERROR: table_to_xvg.pl: table for type non-bonded should begin with 0, >>>> but I found -180 >>>> >>>> How can I do this with dihedrals? >>>> >>>> Steven >>>> >>>> >>>> >>>> >>>> > > -- > 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/groups/opt_out. -- 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/groups/opt_out.
