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scaling factor about the free energy calculations
- xiaoyan_zheng
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8 years 4 months ago #5274
by xiaoyan_zheng
scaling factor about the free energy calculations was created by xiaoyan_zheng
Dear all,
I have a questions about the scaling factor used in martini force field:
We usually use the scaling factor to correct our simulation time, due to acceleration of the coarse grained potential.
Due to the smoother potential function of the CG force field, the corresponding potential energy surface became smoother than all -atomic MD, if we calculate the free energy barrier of some important process using martini force field, do we also need to correct our simulation results by a scaling factor ?
Looking forward to your reply.
Thanks,
Xiaoyan
I have a questions about the scaling factor used in martini force field:
We usually use the scaling factor to correct our simulation time, due to acceleration of the coarse grained potential.
Due to the smoother potential function of the CG force field, the corresponding potential energy surface became smoother than all -atomic MD, if we calculate the free energy barrier of some important process using martini force field, do we also need to correct our simulation results by a scaling factor ?
Looking forward to your reply.
Thanks,
Xiaoyan
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- mnmelo
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8 years 4 months ago #5295
by mnmelo
Replied by mnmelo on topic scaling factor about the free energy calculations
Hi Xiaoyan,
No, there's no need to correct the free energies as the Martini force field was parameterized to correctly reproduce those quantities.
Cheers,
Manel
No, there's no need to correct the free energies as the Martini force field was parameterized to correctly reproduce those quantities.
Cheers,
Manel
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- xiaoyan_zheng
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8 years 4 months ago - 8 years 4 months ago #5296
by xiaoyan_zheng
Replied by xiaoyan_zheng on topic scaling factor about the free energy calculations
Hi Manel,
Thanks for your kind reply. I just want to confirm this case.
Best regards,
Xiaoyan
Thanks for your kind reply. I just want to confirm this case.
Best regards,
Xiaoyan
Last edit: 8 years 4 months ago by xiaoyan_zheng.
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- peterkroon
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8 years 4 months ago #5298
by peterkroon
Replied by peterkroon on topic scaling factor about the free energy calculations
I tend to disagree with Manuel here, Martini is parametrized to reproduce partition free energies, not activation energies. This would mean a scaling factor is indeed required.
That said, it can be that your activation energy is secretly a partition free energy, for example if you're looking at a transition across a membrane. For this and several other reasons, I daren't give any numbers.
That said, it can be that your activation energy is secretly a partition free energy, for example if you're looking at a transition across a membrane. For this and several other reasons, I daren't give any numbers.
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