Dear Tinashe, it might be the way how the unsampled areas are extrapolated. I think the standard is linear interpolation (but i might be wrong on that). You can always change that by using
1) csg_resample --in xxx --out yyy --grid 0:0.001:3 (choose proper grid for your case) 2) csg_call table extrapolate --function quadtratic infile outfile function can be linear,exponetnial, quadratic, ... check the help 3) convert potential to gromacs. However, I don't think that will be an issue since the potential anyways is very large and should never be sampled. In any case, plot the potential and looks whether it looks sensible. If it has an easy functional form, e.g. harmonic, I would recommend fitting a functional form and use these parameters for gromacs input. Best, Victor 2012/2/13 Tinashe <[email protected]>: > I have been trying to reproduce the table_*.xvg files in the propane > tutorial. > > I obtained the bond potentials using csg_boltzmann: > > The following are parts of the "bond.pot.ib" and "bond.xml" files: > > "bond.pot.ib" > 0.152097 21.2962 5895.79 > 0.152405 19.4769 2445.97 > ... > 0.165675 0.0496598 149.931 > 0.165983 0.0142966 80.4637 > 0.166292 0 17.5345 > 0.1666 0.00347479 -44.5805 > 0.166909 0.0275138 -110.011 > ... > 0.180178 20.7073 -2300.42 > 0.180487 21.1912 -3816 > > "bond.xml" > <cg> > <inverse> > <program>gromacs</program> > <gromacs> > <pot_max>1e8</pot_max> > <table_end>3</table_end> > <table_bins>0.002</table_bins> > </gromacs> > </inverse> > </cg> > > I have done the following command to obtain the table_*.xvg file: > > csg_call --options bond.xml --ia-type bonded convert_potential gromacs > bond.pot.ib table_b1.xvg > > and read previous suggestions to Sergio for example concerning ibi > (https://groups.google.com/forum/#!msg/votca/OSaBKQTR7C0/wLAXmbGxw74J) > but I still can't get my table_b1.xvg to match the one in the > tutorial. I would really appreciate any help to resolve this issue. > > Whilst the minimum point coincides, the right and left sides of the > potentials are very steep. > > How is it that the tutorial file intercepts the vertical axis at > 6677.89??? > 0.000000 6677.890000 0 > 0.001000 6595.820000 0 > 0.002000 6514.250000 0 > > I have tried to modify the bin size in the bond.xml and changed the > pot_max value but my table_b1.xvg file is still different??? I surely > have to be doing something wrong, please help me. > > Thanks. > > -- > You received this message because you are subscribed to the Google Groups > "votca" group. > To post to this group, send email to [email protected]. > To unsubscribe from this group, send email to > [email protected]. > For more options, visit this group at > http://groups.google.com/group/votca?hl=en. > -- You received this message because you are subscribed to the Google Groups "votca" group. To post to this group, send email to [email protected]. To unsubscribe from this group, send email to [email protected]. For more options, visit this group at http://groups.google.com/group/votca?hl=en.
