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. 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.
