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At first thanks for your tool for calculating several membrane parameters.
With the recent removal of support for calculating the order parameter of unsaturated chains with gromacs gmx order tool, we are trying to migrate to g_lomepro. We found a few issues:
When trying to calculate the order parameter for the unsaturated chain, we were wrongly obtaining the values only for the atoms around the unsaturation. Later, I saw this commit: ff0413b
And, indeed, that was the issue and now it works fine for us. We wonder if maybe the "develop" and "master" branches could be finally merged to prevent people from using the a bogus version by mistake.
Those lipids have 4 unsaturated changes. For now we are simply calculating the order for one chain, but maybe other people could welcome the support for -unsat 3 and 4 (if it is not too hard to implement)
When looking at the averaged order .dat files, we see that there is one column showing the (expected) order parameter, but we don't understand what the second column represents. Could that be documented somewhere?
Thanks a lot and best regards
The text was updated successfully, but these errors were encountered:
Hello,
At first thanks for your tool for calculating several membrane parameters.
With the recent removal of support for calculating the order parameter of unsaturated chains with gromacs gmx order tool, we are trying to migrate to g_lomepro. We found a few issues:
When trying to calculate the order parameter for the unsaturated chain, we were wrongly obtaining the values only for the atoms around the unsaturation. Later, I saw this commit:
ff0413b
And, indeed, that was the issue and now it works fine for us. We wonder if maybe the "develop" and "master" branches could be finally merged to prevent people from using the a bogus version by mistake.
We sometimes work with TOCL2 lipid:
https://charmm-gui.org/archive/lipid/tocl2.gif
Those lipids have 4 unsaturated changes. For now we are simply calculating the order for one chain, but maybe other people could welcome the support for -unsat 3 and 4 (if it is not too hard to implement)
Thanks a lot and best regards
The text was updated successfully, but these errors were encountered: