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Mapping quercetin in martini 3 bead
- simjang04
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1 year 2 weeks ago #9605
by simjang04
Mapping quercetin in martini 3 bead was created by simjang04
Hello,
I'm so sorry about writing this type of question, which like, 'I can't do it! help me!' like kid.
but i'm struggling on this issue about two months, so I REALLY need help from anyone.
as I wrote, I'm trying to parametrize quercetin(in correct, ionized quercetin. two hydrogen removed, from two -OH near by carbonyl group.) in martini 3,
I tried so many ways in changing mapping methods, beadtypes, constraints lengths, applying improper dihedrals etc, as I can do, but always results was SegFault on gromacs or LINCS error, bond rotation error, etc.
I think this is due to instability of system, by my mapping, because given martini 3 tutorial molecule was successfully completed mdrun.
so, I need help. any recommendation or advise will be helpful.
thank you and sorry again.
I'm so sorry about writing this type of question, which like, 'I can't do it! help me!' like kid.
but i'm struggling on this issue about two months, so I REALLY need help from anyone.
as I wrote, I'm trying to parametrize quercetin(in correct, ionized quercetin. two hydrogen removed, from two -OH near by carbonyl group.) in martini 3,
I tried so many ways in changing mapping methods, beadtypes, constraints lengths, applying improper dihedrals etc, as I can do, but always results was SegFault on gromacs or LINCS error, bond rotation error, etc.
I think this is due to instability of system, by my mapping, because given martini 3 tutorial molecule was successfully completed mdrun.
so, I need help. any recommendation or advise will be helpful.
thank you and sorry again.
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- riccardo
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1 year 1 day ago #9617
by riccardo
Replied by riccardo on topic Mapping quercetin in martini 3 bead
You may need some bonded construction as described in Figure 3c in
onlinelibrary.wiley.com/doi/epdf/10.1002/adts.202100391
in order to make the model numerically stable.
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