2016-05-16 15:00 GMT-06:00 Chang Woon Jang <[email protected]>: > Dear VOTCA users, > > > I need a help to use pressure correction during nonbond IBI > calculation. Without the pressure correction, the derived CG potentials do > not give the right density close to experiment. The density is much lower > than the experiment. Therefore, I would like to re-derive nonbond potentials > using pressure correction. The previous setting.xml for nonbond IBI is like > below for example. Where do I need to put the <p_target>, <post_update>, > <pressure>, <type>, etc? Do I need to put those blocks in the <inverse> > block? > > I am not sure the syntax for the pressure correction. Would you please give > me a comment or example script? Thank you very much. See the spce/ibi_pressure tutorial: https://github.com/votca/csg-tutorials/tree/master/spce/ibi_pressure
The p_target goes into the inverse block and the pressure block under the post_update_options option. Christoph > > <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>0.32</min> > <max>1.47</max> > <step>0.01</step> > <inverse> > <!-- target distribution (rdf), just give gromas rdf.xvg --> > <target>CG-CG.A-A.dist.tgt</target> > <!-- update cycles --> > <do_potential>1 0 0 0 0 0 0 0 0 0 0 0 0 0 0</do_potential> > <!-- additional post processing of dU before added to potential --> > <post_update></post_update> > <!-- additional post processing of U after dU 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> > > > Best regards, > Changwoon Jang, > > -- > 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 https://groups.google.com/group/votca. > For more options, visit https://groups.google.com/d/optout. -- 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 https://groups.google.com/group/votca. For more options, visit https://groups.google.com/d/optout.
