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Some Questions regarding with Cholesterol model
- yuxiang900599015
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8 years 8 months ago #4787
by yuxiang900599015
Some Questions regarding with Cholesterol model was created by yuxiang900599015
Dear all,
I'm wondering whether the older version of cholesterol (martini_v2.0_CHOL_01.itp) could be a substitute of dry martini version (dry_martini_v2.1_cholesterol.itp) in an implicit solvent environment. I'm asking this question, because I'm currently using lammps and there is no substitute of virtual_site function of new version in lammps.
Thank you
I'm wondering whether the older version of cholesterol (martini_v2.0_CHOL_01.itp) could be a substitute of dry martini version (dry_martini_v2.1_cholesterol.itp) in an implicit solvent environment. I'm asking this question, because I'm currently using lammps and there is no substitute of virtual_site function of new version in lammps.
Thank you
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- mnmelo
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8 years 7 months ago #4837
by mnmelo
Replied by mnmelo on topic Some Questions regarding with Cholesterol model
Hello,
Well, as described in the Dry Martini paper, there were some modifications to the cholesterol topology besides converting it to virtual-sites. The protrusion of beads R1 and R5 was increased so as to keep the fluidizing properties of cholesterol.
While the old model can be used with Dry Martini, it doesn't have such improvements, so I'd recommend against using it.
You may try, however, to modify the old model so that protrusion distances are increased, to match the extra 60% of the new model. These 60% correspond to an extra 0.52 Angstrom in the distance between R1 and the plane ROH-R2-R3, and an extra 0.66 Angstrom between R5 and the R2-R3-C1.
Good luck!
Manel
Well, as described in the Dry Martini paper, there were some modifications to the cholesterol topology besides converting it to virtual-sites. The protrusion of beads R1 and R5 was increased so as to keep the fluidizing properties of cholesterol.
While the old model can be used with Dry Martini, it doesn't have such improvements, so I'd recommend against using it.
You may try, however, to modify the old model so that protrusion distances are increased, to match the extra 60% of the new model. These 60% correspond to an extra 0.52 Angstrom in the distance between R1 and the plane ROH-R2-R3, and an extra 0.66 Angstrom between R5 and the R2-R3-C1.
Good luck!
Manel
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