mapping two different molecules for ibi

[Saeed Norouzi]

Dear Christoph and votca users,

I am trying to do a CG model for my polymer system and nanoparticle. The CG model for the pure polymer is done using ibi. Now I need to find the interaction between the nanoparticle and polymer (do ibi for non-bond interaction between the particle beads and polymer). I have created the all-atom topology and mapping file for the polymer (molecule name is DEOAA in .xml file) and also for the nanoparticle (molecule name is particle in the .xml file). csg_map command (csg_map --top AA-topology.xml --trj no_bpc.xtc --out traj-CG.dump --cg A2Cmapping.xml ) runs successfully, but the problem is that the CG trajectory does not include the nanoparticle structure (only shows the polymer which is type A B C). My particles also have three types P4 P5 P6.

PS: the particle is mapped to 104 beads and each polymer chain includes 13 beads. 

I have attached the topology and mapping file here. I appreciate your help.

Best regards

saeed

[Christoph Junghans]

For two molecules you will need to call csg_map with two mapping
files, e.g. csg_map .... --cg "map1.xml;map2.xml".

Christoph

>
> Best regards
> saeed
>
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--
Christoph Junghans
Web: http://www.compphys.de

[Saeed Norouzi]

Dear Christoph,

Thank you for your help. I made two map files and now I have the target distributions. Now, I am trying to do the iteration part and I have an error again on the mapping part. I build two CG mapping files (CG-CG-mapping-polymer.xml;CG-CG-mapping-particle.xml) for polymer and particle. Also, in the setting file I have specified those two by <map>CG-CG-mapping-polymer.xml;CG-CG-mapping-particle.xml</map>/ 

So far everything seems fine to me, but there is an error regarding bonded interaction that I cannot fix. I only have 3 non-bond potentials which need to be matched with the target, and I have no idea what it means for bonded interaction. 

I attached the setting file, map files for CG, log file and also my CG trajectory file here. 

I would really appreciate your help with this.

PS: I also tried this command (csg_stat --nt 24 --options /data/snorouzi/data/3-PLA/ibi_PLA/nano_particle/settings.xml --top CG-topolgy.xml --trj traj.dump --begin 0 --first-frame 0 --cg /data/snorouzi/data/3-PLA/ibi_PLA/nano_particle/"CG-CG-mapping-particle.xml;CG-CG-mapping-polymer.xml")  the error is "cannot find: <109> in DEOAA an error occurred: error while trying to create bonded interaction, bead 109 not found" which still I could not see what it means by  creating bonded interaction.

########################################################################################################################################
#                                                                                                                                      #
# ERROR:                                                                                                                               #
# calc_rdf_generic.sh: Mapping file 'CG-CG-mapping-polymer.xml;CG-CG-mapping-particle.xml' for bonded interaction not found in maindir #
# For details see the logfile /data/snorouzi/data/3-PLA/ibi_PLA/nano_particle/inverse.log                                              #
#                                                                                                                                      #
########################################################################################################################################
die: (called from 11538)  CSG_MASTER_PID is 7773
die: pids to kill:  7773 11417 11523 11538

Best regards

Saeed

To view this discussion on the web visit https://groups.google.com/d/msgid/votca/CAHG27e4GvmL73cAKM52uPxq2OuwAkH19w%3Dm_Tv52ktWMLjz5vg%40mail.gmail.com.

[Christoph Junghans]

On Wed, Sep 27, 2023 at 6:55 AM Saeed Norouzi <norou...@gmail.com> wrote:
>
> Dear Christoph,
>
> Thank you for your help. I made two map files and now I have the target distributions. Now, I am trying to do the iteration part and I have an error again on the mapping part. I build two CG mapping files (CG-CG-mapping-polymer.xml;CG-CG-mapping-particle.xml) for polymer and particle. Also, in the setting file I have specified those two by <map>CG-CG-mapping-polymer.xml;CG-CG-mapping-particle.xml</map>/
>
> So far everything seems fine to me, but there is an error regarding bonded interaction that I cannot fix. I only have 3 non-bond potentials which need to be matched with the target, and I have no idea what it means for bonded interaction.
>
> I attached the setting file, map files for CG, log file and also my CG trajectory file here.
>
> I would really appreciate your help with this.

First of all if you don't plan to do IBI on the bonded interaction,
you won't need a mapping file.

The error hints at a typo in the mapping file.
I would run
$ csg_dump -top CG-topolgy.xml --cg
/data/snorouzi/data/3-PLA/ibi_PLA/nano_particle/"CG-CG-mapping-particle.xml;CG-CG-mapping-polymer.xml
to see what VOTCA reads.

Christoph

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