that use your tool to analyze simulation involving peptides but, when I read your tutorial, I found that, supposedely, membplugin doesn't handle that cases (simulations involving anything else than lipids): https://sourceforge.net/projects/membplugin/files/Tutorial/intro_SDPCandCHOL_v3.pdf/download
Second point, page 2:
"Do not use or use the
MEMBPLUGIN with caution to analyse membranes with:
1. significant curvature or undulations. Our codes assume that the membrane is flat
and rests in the xy-plane. If this is not the case the results of each tool will be
affected. The larger the undulations the higher will be the deviations in respect to
the expected value. Therefore, unless you understand what you are doing refrain
yourself from using the plug-in for such systems.
2. systems containing additional non-lipid molecules. In the current release the MEM-
BPLUGIN tools are not aware of the presence of proteins or any other non-lipid
compounds in the membrane. Some analysis tools, e.g. area per lipid, can be
wrongly affected by this. In a future release we plan to make all tools agnostic to
such non-lipid molecules. Until then bear in mind this issue.
3. non-rectangular periodic boundary conditions (PBC)."
I don't know then if there is an "standardized" way to workaround that issue, or if the issue was fixed at some point.
Thanks a lot for your help
If you would like to refer to this comment somewhere else in this project, copy and paste the following link:
Currently, there is no way to overcome these 3 cases with MEMBPLUGIN.
We will update the tutorial and wiki page if we manage to address those cases in the future.
Best regards,
Ismael.
If you would like to refer to this comment somewhere else in this project, copy and paste the following link:
Hello,
I discovered your plugin while reading papers like:
https://pubs.rsc.org/en/content/articlelanding/2017/CP/C7CP01941F#!divAbstract
that use your tool to analyze simulation involving peptides but, when I read your tutorial, I found that, supposedely, membplugin doesn't handle that cases (simulations involving anything else than lipids):
https://sourceforge.net/projects/membplugin/files/Tutorial/intro_SDPCandCHOL_v3.pdf/download
Second point, page 2:
"Do not use or use the
MEMBPLUGIN with caution to analyse membranes with:
1. significant curvature or undulations. Our codes assume that the membrane is flat
and rests in the xy-plane. If this is not the case the results of each tool will be
affected. The larger the undulations the higher will be the deviations in respect to
the expected value. Therefore, unless you understand what you are doing refrain
yourself from using the plug-in for such systems.
2. systems containing additional non-lipid molecules. In the current release the MEM-
BPLUGIN tools are not aware of the presence of proteins or any other non-lipid
compounds in the membrane. Some analysis tools, e.g. area per lipid, can be
wrongly affected by this. In a future release we plan to make all tools agnostic to
such non-lipid molecules. Until then bear in mind this issue.
3. non-rectangular periodic boundary conditions (PBC)."
I don't know then if there is an "standardized" way to workaround that issue, or if the issue was fixed at some point.
Thanks a lot for your help
Dear Pacho,
Currently, there is no way to overcome these 3 cases with MEMBPLUGIN.
We will update the tutorial and wiki page if we manage to address those cases in the future.
Best regards,
Ismael.
OK, thanks a lot for the clarification