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?
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] <javascript:>>:
>
> > 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] <javascript:>.
> > To post to this group, send email to [email protected]
> <javascript:>.
> > 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.
