thank you. I just wanted after resample to make a table for gromacs. I just removed "o" and placed "i" so extrapolation was not performed. I changed radians to degrees.
Steven On Thursday, August 15, 2013 4:38:04 PM UTC+1, Christoph Junghans wrote: > > 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] <javascript:>>: > > 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]: > >> > >> 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]: > >>> > >>> 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]: > >>>> > >>>> > >>>> > >>>> On Thursday, August 15, 2013 1:08:58 PM UTC+1, [email protected]: > >>>>> > >>>>> 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] <javascript:>. > > To post to this group, send email to [email protected]<javascript:>. > > > 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.
