2013/9/17 Chandan Choudhury <[email protected]>: > 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
I don't really see what would be the use of this! csg_resample and extrapolate are already done inside "convert_potential gromacs". If you want to smooth your potential (1st command), you could simply add the "smooth" task to the post_update list of the bonded interaction. Having that said, you can of course, write a custom postupd script, which runs the 3 command from above. > > > 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. -- 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.
