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PCA analysis
- Carla
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12 years 10 months ago #731
by Carla
PCA analysis was created by Carla
Hi,
I would like to know if someone have already done the PCA or/and DynDom analysis in CG simulations.
I am able to do g_covar in GROMACS, however I receive Segmentation Fault message when I perform g_anaeig.
Whether someone knows how can I do it, please inform me.
Best regards,
Carla
I would like to know if someone have already done the PCA or/and DynDom analysis in CG simulations.
I am able to do g_covar in GROMACS, however I receive Segmentation Fault message when I perform g_anaeig.
Whether someone knows how can I do it, please inform me.
Best regards,
Carla
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- xavier
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12 years 9 months ago #735
by xavier
The PCA should work as for any other system. I guess the error you are seeing is due to the manner you use topologies/index/gro file/ ...
For DynDom, it is unfortunate that the code uses the backbone atoms which are missing in the CG topology, consequently DynDom can not use a CG coordinate file. Alternatively you can rebuild the backbone using a classic algorithm of backbone reconstruction.
On possibility is to use the reverse transformation as we use to back-map the CG to atomistic resolution. Other possibilities are available but I am not familiar with them. I have been suggested maxsprout once.
Actually I just remember that DynDom3D works on a set of Calphas ...
XAvier.
Replied by xavier on topic PCA analysis
Carla wrote: Hi,
I would like to know if someone have already done the PCA or/and DynDom analysis in CG simulations.
I am able to do g_covar in GROMACS, however I receive Segmentation Fault message when I perform g_anaeig.
Whether someone knows how can I do it, please inform me.
Best regards,
Carla
The PCA should work as for any other system. I guess the error you are seeing is due to the manner you use topologies/index/gro file/ ...
For DynDom, it is unfortunate that the code uses the backbone atoms which are missing in the CG topology, consequently DynDom can not use a CG coordinate file. Alternatively you can rebuild the backbone using a classic algorithm of backbone reconstruction.
On possibility is to use the reverse transformation as we use to back-map the CG to atomistic resolution. Other possibilities are available but I am not familiar with them. I have been suggested maxsprout once.
Actually I just remember that DynDom3D works on a set of Calphas ...
XAvier.
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