On Fri, Mar 15, 2013 at 7:58 PM, Christoph Junghans <[email protected]>wrote:
> 2013/3/15 Chandan Choudhury <[email protected]>: > > Dear votca users, > > > > In the hexane tutorials, there exists a setting.xml in ibi_bonded folder. > > Its snippet are as follows : > > <cg> > > <bonded> > > <!-- name of the interaction --> > > <name>AB.bond</name> > > <!-- fmatch specific stuff --> > > <min>0.21</min> > > <max>0.285</max> > > <step>0.005</step> > > <inverse> > > <!-- target distribution --> > > <target>AB.dist.tgt</target> > > <gromacs> > > <table>table_b0.xvg</table> > > </gromacs> > > </inverse> > > </bonded> > > ... > > ... > > </cg> > > > > Does the section of min and max are required fof IBI steps or does it is > > only necessary force matching (FM) steps (when FM is used)? If the > sections > > are necessary for IBI, then from where to obtain these values from? > First of all the comment is actually misleading/wrong, this has > nothing to do with force matching. > Thanks Christoph for making it very clear. > Second, ibi_bonded can only be done with votca-1.3, so make sure you > have the right version. > I am using 1.2.3 with gmx 4.5.5 Between min and max, the IBI update gets performed. We usually > determine these number from the target distribution. > min should be a an r where g(r) > 0 and max should be an r where g(r) > has a minimum or is close to one. > step should be chosen such that the statistics in the cg run is enough > to calculate a smooth rdf, so something between 0.005 and 0.01. > > Christoph > > > > > > > Chandan > > > > -- > > Chandan kumar Choudhury > > NCL, Pune > > INDIA > > > > -- > > 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?hl=en. > > 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?hl=en. > For more options, visit https://groups.google.com/groups/opt_out. > > > -- Chandan kumar Choudhury NCL, Pune INDIA -- 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?hl=en. For more options, visit https://groups.google.com/groups/opt_out.
