2015-11-23 5:45 GMT-07:00 frank Zack <[email protected]>: > Thank you Christoph for your Suggestions. I'll try a bigger scale factor. > BTW: I was wondering if wjk pressure-correction does a better job in this > case....However, i couldnt find out where to put the > "<paricle_dens>...</particle_dens> tags.. > I tried to include it in my "bond"-block: > .... > <bonded> > <name>bond</name> > <min>0.200175</min> > <max>0.549825</max> > <step>0.00035</step> > <inverse> > <target>bond.dist.tgt</target> > <p_target>1.0</p_target> > <post_update>pressure</post_update> > <do_potential>0 1 0</do_potential> > <post_update_options> > <pressure> > <type>wjk</type> > <do>1 1 1</do> > <wjk> > <scale>0.05</scale> > <particle_dens>1.1</particle_dens> > </wjk> > </pressure> > </post_update_options> > <lammps> > <table>bond.pot</table> > </lammps> > </inverse> > </bonded> > > ...as well as into the inverse-block: > > <inverse> > <kBT>2.49435</kBT> > <particle_dens>1.1</particle_dens> > <program>lammps</program> > <lammps> > <script>my.in</script> > <topol>topol.xml</topol> > <traj>traj.dump</traj> > </lammps> > <initial_configuration>maindir</initial_configuration> > <filelist>conv_tables.sh my.in cg_50x300.data topol.xml cg.dump > eval_press.sh</filelist> > <iterations_max>60</iterations_max> > <method>ibi</method> > <log_file>inverse.log</log_file> > <map>mapping.xml</map> > </inverse> > </cg> > > I guess Im not providing the value at the correct place in my settings.xml? I guess you got an error like: "csg_get_interaction_property: Could not get 'inverse.particle_dens' for interaction with name...", which basically means that the particle_dens field should go directly in the inverse block of the interaction (hence the path "inverse.particle_dens"). I can turn the spce/ibi_pressure tutorials into using the wjk correction with the following patch: --- a/spce/ibi_pressure/settings.xml +++ b/spce/ibi_pressure/settings.xml @@ -15,17 +15,18 @@ <target>CG-CG.dist.tgt</target> <!-- target pressure --> <p_target>1.0</p_target> + <particle_dens>3.2965079</particle_dens> <!-- update cycles --> <do_potential>0 1 0</do_potential> <!-- additional post processing of dU before added to potential --> <post_update>pressure</post_update> <post_update_options> <pressure> - <type>simple</type> + <type>wjk</type> <do>1 0 1</do> - <simple> - <scale>0.0003</scale> - </simple> + <wjk> + <scale>1</scale> + </wjk> </pressure> </post_update_options> <!-- additional post processing of U after dU added to potential -->
You can set scale to 1 as it is just an extra scaling factor for A (Eq. 7 in http://dx.doi.org/10.1140/epje/i2008-10413-5) Christoph > > Regards,frank. > > > Am Sonntag, 22. November 2015 18:09:34 UTC+1 schrieb Christoph Junghans: >> >> 2015-11-19 14:00 GMT-07:00 frank Zack <[email protected]>: >> > Hi all, >> > Ive got some general question.some of my coarse grained polymers show >> > rising pressure during ibi while for others the simple pressure correction >> > drives the pressure towards my target 1atm. Have u ever encountered similar >> > troubles? What might be the reason?bad target distributions? Bad inversion >> > timing? In my case i applied the correction to 3 nonbonded interactions >> > successively. The first 3-6 steps the pressure is continuously reduced from >> > 60 to 40 atm. After that it rises again as the pair-distris get closer to >> > my >> > targets. Any suggestions? >> I have no good idea, but you might need to increase the prefactor to a >> bigger value or do the pressure correction without IBI for a while. >> >> > >> > 2nd question: Is there any rule of thumb of how big my coarse grained >> > system is? If im coarse-graining polymers i usually use relatively low >> > molecular mass initial configurations like 100 chains each having 100 >> > repeating units...if i recognize im unable to properly equilibrate the >> > system i use even shorter chains. however, as im interested in the effects >> > of entanglement i always try to keep the chain lengths above some critical >> > value in order to get a high molecular weight between chain entanglements >> > as >> > compared to molec weight (prim path analysis). >> > Have you ever tried to coarse grain polymers? I would highly appreciate >> > if you can you share your experience regarding chain length.. >> That is not my main expertise, but certainly people are working on >> better equilibration techniques like: >> <http://pubs.acs.org/doi/abs/10.1021/mz5000015> >> >> Christoph >> >> > >> > Regards, >> > Frank >> > >> > -- >> > 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/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 http://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 http://groups.google.com/group/votca. For more options, visit https://groups.google.com/d/optout.
