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SCFix - Martini 3.0.0
- Marius
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2 years 6 months ago #9186
by Marius
SCFix - Martini 3.0.0 was created by Marius
Hi everybody,
I was wondering if the scfix must be applied to every protein structure simulated with MARTINI 3.0. Was it also used during the validation of the force field or is it just a feature which improves the accuracy of the model only in specific cases (e.g. peripheral membrane-proteins, beta-sheets)?
The reference structure seems to have a strong influence on the correction potential. I understand the assumption that the fix should work well for experimental derived structures (X-Ray, NMR, etc.), but couldn't it bias the coarse grained simulation if we fix a side chain in a maybe "non-ideal" conformation?
Thanks in advance,
Marius
I was wondering if the scfix must be applied to every protein structure simulated with MARTINI 3.0. Was it also used during the validation of the force field or is it just a feature which improves the accuracy of the model only in specific cases (e.g. peripheral membrane-proteins, beta-sheets)?
The reference structure seems to have a strong influence on the correction potential. I understand the assumption that the fix should work well for experimental derived structures (X-Ray, NMR, etc.), but couldn't it bias the coarse grained simulation if we fix a side chain in a maybe "non-ideal" conformation?
Thanks in advance,
Marius
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