Dear votca users, In continuation of the discussion, is it possible to use the methodology of 1.2.3 version to create the tab. pot. (esp. for bonds) in each step (for 1.3-dev). In 1.2.3, it is done manually, and this has been discussed number of times in the mailing list. Can this steps be incorporated in 1.3-dev version.
The commands which I use for 1.2.3 version are as follows: csg_call table smooth $1.bond.cut $1.bond.smooth csg_resample --in $1.bond.smooth --out $1.bond.refined --grid 0::0.001:0.5 csg_call table extrapolate --function quadratic $1.bond.refined $1.bond.pot.cur csg_call --ia-type bonded --ia-name $1.bond --options convert.xml convert_potential gromacs Chandan -- Chandan kumar Choudhury NCL, Pune INDIA On Sat, Sep 14, 2013 at 11:33 AM, Chandan Choudhury <[email protected]>wrote: > > On Sat, Sep 14, 2013 at 1:15 AM, Christoph Junghans <[email protected]>wrote: > >> 2013/9/13 Chandan Choudhury <[email protected]>: >> > >> > Dear Christoph, >> > >> > I am attaching the bonded distribution of BC bond and the corresponding >> > potentials. The distributions show the sudden increase and there is >> also a >> > discontinuity in the potentials, Can you suggest me how can this be >> avoided. >> This is not exactly a discontinuity, the slops is just slightly higher >> for smaller r. >> Also, have a look if the correspond table_b*.xvg is okay. >> > > I am attaching the table_b1.xvg for the steps from 001 to 004. This > corresponds to the BC.bond. Around the min 0.354 and and 0.355 the table > has a jump in potential. > > I would also check the full distributions (copy your settings.xml, and >> change min to 0 and max to bigger number and run csg_stat manually in >> a iteration step.) >> > > The full distribution does not show such abrupt increase. > >> >> You could also increase r min to 0.355, as there is anyway not much >> information in the last bin. >> > > Increasing min to 0.355 or 0.358 does not help. There is a sudden rise in > the potential (BC.bond.pot.new), distributions and table.b1.xvg. > > Isn't seems unusual to have a rise in distributions at the r min, anyways > the rise is not found in the full distributions? > > Chandan > >> >> 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/groups/opt_out.
