bond.dist.tgt validation

[Akash Banerjee]

Hi Votca Development team,

I am trying to validate the coarse grained bond distributions against the all-atom bond distributions. In my case, the bond.dist.tgt file ( dumped by using csg_stat on all atom files) gives different results as compared to using my own analysis tool.

I am assuming the bond.dist.tgt files have been generated using a Center of Mass framework for all coarse grained fragments. 

Also, I used the GROMACS analysis tool to find the bonded distribution in the all-atom model. The result turned out to be very different from bond.dist.tgt. 

Please help me understand how bond.dist.tgt is derived. This information would help me validate distributions between AA and CG scales.

Thank you for your help in advance.

Kind Regards,

Akash

[Christoph Junghans]

On Tue, May 19, 2020 at 11:58 AM Akash Banerjee <akas...@gmail.com> wrote:
>
> Hi Votca Development team,
>
> I am trying to validate the coarse grained bond distributions against the all-atom bond distributions. In my case, the bond.dist.tgt file ( dumped by using csg_stat on all atom files) gives different results as compared to using my own analysis tool.
> I am assuming the bond.dist.tgt files have been generated using a Center of Mass framework for all coarse grained fragments.

For VOTCA the mapping is whatever you put in the mapping file, it
isn't COM by default.

> Also, I used the GROMACS analysis tool to find the bonded distribution in the all-atom model. The result turned out to be very different from bond.dist.tgt.
>
> Please help me understand how bond.dist.tgt is derived. This information would help me validate distributions between AA and CG scales.

The first step would be to check if your mapping is right, you could
run csg_map on the initial condition (conf.gro) and then overlay the
output in VMD to see if the cg beads are in the right spots.

Christoph

>
> Thank you for your help in advance.
>
> Kind Regards,
> Akash
>

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--
Christoph Junghans
Web: http://www.compphys.de

[Akash Banerjee]

Thank you Christoph for your help. I figured the issue out using csg_map.

Thank you again for your guidance and support.

Thank you

Kind Regards,

Akash 

To view this discussion on the web visit https://groups.google.com/d/msgid/votca/CAHG27e4YxrJXOtT-GhMKwQm2-ANuf%2BTQ2SEbQmyfT%3DNv%2B5iSLQ%40mail.gmail.com.