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MARTINI2.3P, MARTINI2.2refP and MARTINI2.2polIon
- konarkb
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2 years 10 months ago #8989
by konarkb
MARTINI2.3P, MARTINI2.2refP and MARTINI2.2polIon was created by konarkb
I wanted to use Martini 2.3P for my simulations. But there is no option in martinize2 to use martini23p for forcefields, i.e. -ff martini23p is not possible. So, how can I martinize a molecule using martinize2 for martini2.3P forcefields?
Is there any separate forcefields and mapping files for martini2.3P?
Or is it sufficient to use -ff martini22p as an option in martinize2 and then use martini 2.3P itp files in the topology file?
Is there any separate forcefields and mapping files for martini2.3P?
Or is it sufficient to use -ff martini22p as an option in martinize2 and then use martini 2.3P itp files in the topology file?
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- konarkb
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2 years 10 months ago - 2 years 10 months ago #8992
by konarkb
Replied by konarkb on topic MARTINI2.3P, MARTINI2.2refP and MARTINI2.2polIon
I have the same question for the MARTINI2.2refP and MARTINI2.2polIon versions?
Last edit: 2 years 10 months ago by konarkb.
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- riccardo
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2 years 10 months ago #8993
by riccardo
Replied by riccardo on topic MARTINI2.3P, MARTINI2.2refP and MARTINI2.2polIon
Yep, I think none of these are implemented in martinize2. You could open an issue about this on the github of martinize2 (
github.com/marrink-lab/vermouth-martinize/issues
) or maybe even contribute the implementation yourself via a pull request.
Regarding martini2.3P, what does the paper ( pubs.acs.org/doi/abs/10.1021/acs.jctc.9b01194 ) say about generating models with this version?
I'm not very familiar with any of the versions, so I don't know how they exactly differ from martini 2.2P. For the ones that differ only on the values of few parameters (i.e., where there are no new beads or models defined for amino acids or such), then maybe the older martinize version + the appropriate particle definitions (which can be found all here: cgmartini.nl/index.php/force-field-param...particle-definitions ) do the job.
Regarding martini2.3P, what does the paper ( pubs.acs.org/doi/abs/10.1021/acs.jctc.9b01194 ) say about generating models with this version?
I'm not very familiar with any of the versions, so I don't know how they exactly differ from martini 2.2P. For the ones that differ only on the values of few parameters (i.e., where there are no new beads or models defined for amino acids or such), then maybe the older martinize version + the appropriate particle definitions (which can be found all here: cgmartini.nl/index.php/force-field-param...particle-definitions ) do the job.
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