2013/8/15 Chandan Choudhury <[email protected]>: > On Thu, Aug 15, 2013 at 2:17 AM, Christoph Junghans <[email protected]> > wrote: >> >> 2013/8/14 Chandan Choudhury <[email protected]>: >> > Dear users, >> > >> > Is it possible just to iterate the bonded part (IBI, 1.3-dev). As I see >> > that >> > the convergence check might not work as : >> > >> > the xml options for postadd_acc_convergence.sh are >> > cg.non-bonded.name >> > >> > and for postadd_convergence.sh are >> > cg.inverse.method >> > cg.non-bonded.inverse.post_add_options.convergence.base >> > cg.non-bonded.inverse.post_add_options.convergence.norm >> > cg.non-bonded.inverse.post_add_options.convergence.weight >> > cg.non-bonded.inverse.post_add_options.convergence.what >> > cg.non-bonded.inverse.target >> > cg.non-bonded.max >> > cg.non-bonded.min >> > cg.non-bonded.name >> > cg.non-bonded.step >> > >> > Any light on this would be very helpful. >> postadd script work for bonded interaction, too, by default, just give it >> a try. >> If the manual refers to cg.non-bonded, cg.bonded is implied. (I need >> to fix the manual!) >> >> Back to your question, 2 options: >> >> 1.) If you put only bonded interaction into your settings file only >> bonded interactions will be iterated. >> 2.) You could do_potential=0 for all non-bonded, if you still want to >> have the rdfs calculated. > > > Thanks for your very helpful reply. I am using the option 2. > > I did do_potential=0 for all the non-bonded terms. I have also removed the > convergence from the post add list therein. And added the convergence to the > post add list only on the bonds with the following xml tags: > > <bonded> > <!-- name of the interaction --> > <name>AB.bond</name> > <min>0.30</min> > <max>0.54</max> > <step>0.001</step> > <inverse> > <!-- target distribution --> > <target>AB.bond.dist.tgt</target> > <!-- update cycles --> > <do_potential>1 0 0 0 0</do_potential> > <post_add>convergence</post_add> > <!-- name of the table for gromacs run --> > <gromacs> > <table>table_b0.xvg</table> > </gromacs> > </inverse> > </bonded> > > and remove the post_add tags from all the non bonded terms: > > <non-bonded> > <!-- name of the interaction --> > <name>A-A</name> > <!-- types involved in this interaction --> > <type1>A</type1> > <type2>A</type2> > <!-- dimension + grid spacing of tables for calculations --> > <min>0.00</min> > <max>1.50</max> > <step>0.01</step> > <inverse> > <!-- target distribution (rdf), just give gromas rdf.xvg --> > <target>A-A.dist.tgt</target> > <!-- update cycles --> > <do_potential>0 0 0</do_potential> > <!-- additional post processing of dU before added to potential --> > <!--post_add>convergence</post_add--> > <!-- name of the table for gromacs run --> > <gromacs> > <table>table_A_A.xvg</table> > </gromacs> > </inverse> > </non-bonded> > > The convergence check in cg.inverse are as follows: > > <convergence_check> > <type>default</type> > <limit>0.100</limit> > </convergence_check> > > Upon doing so, I encounter the following error > > ******************************************************* > step 1 done, needed 133 secs > Doing convergence check: default > Running subscript 'convergence_check_default.sh' (from tags > convergence_check default) dir > /opt/apps/votca/1.3-dev/share/votca/scripts/inverse > > Callstack: > /opt/apps/votca/1.3-dev/share/votca/scripts/inverse/inverse.sh - linenumber > 289 > do_external - linenumber 171 in > /opt/apps/votca/1.3-dev/share/votca/scripts/inverse/functions_common.sh > > /opt/apps/votca/1.3-dev/share/votca/scripts/inverse/convergence_check_default.sh > - linenumber 41 > die - linenumber 2 (see 'csg_call --cat function die') > ################################################################################################################## > # > # > # ERROR: > # > # convergence_check_default.sh: No convergence file found! > # > # Have you added convergence to the postadd list of at least one > interaction? # > # For details see the logfile > /data/home/chandan/Documents/votca/polycarbonate/trimer/new_mapping/re/inverse.log > # > # > # > ################################################################################################################## > > What modification should be done in the setting file to overcome this? A > hint would be very helpful. You were absolutely right, for some reason I disabled postupd and postadd routines for bonded interactions! I fixed that in the code: <https://code.google.com/p/votca/source/detail?r=2dc28dda57e5652f10d9d070bb3784204da856ac&repo=csg>
I am sorry for the problems, but you are the first user to actually use bonded IBI. > > Chandan > >> >> Christoph >> > >> > Chndan >> > >> > -- >> > 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. >> > 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. > > > -- > 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.
