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Calculating PMF for umbrella sampling
- SNEHA
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5 years 11 months ago #7654
by SNEHA
Calculating PMF for umbrella sampling was created by SNEHA
Hi all,
I have performed Steered MD to pull ligand from one terminal to other through the tunnel that traverses along the length of my protein. For this, I performed SMD in 3 parts
1. To pull from N terminal to central part
2. From central region upto C-terminal
3. From C-terminal, it was pushed away from the protein into the water box
I have used different protein residues as reference for all these 3 parts.
Now I picked frames from each part and performed umbrella sampling. I have PMF for individual part
However, how can I calculate PMF for the entire path? Can I manually add PMF for each part ?
Kindly help
I have performed Steered MD to pull ligand from one terminal to other through the tunnel that traverses along the length of my protein. For this, I performed SMD in 3 parts
1. To pull from N terminal to central part
2. From central region upto C-terminal
3. From C-terminal, it was pushed away from the protein into the water box
I have used different protein residues as reference for all these 3 parts.
Now I picked frames from each part and performed umbrella sampling. I have PMF for individual part
However, how can I calculate PMF for the entire path? Can I manually add PMF for each part ?
Kindly help
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- Pim
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5 years 11 months ago #7668
by Pim
Replied by Pim on topic Calculating PMF for umbrella sampling
Hi, this doesn't really appear to be a Martini question, so you might want to find help elsewhere, but here is a small tip:
In the ideal case where you really sampled the complete space you have the true state free energies, so then you can just manually add the PMFs together if you use the same reaction coordinate. However, you've used different residues, so this is not correct. I don't know how to do it properly, if it is possible at all.
A nice recent paper where they show an example of how to report it is this one: www.nature.com/articles/s41467-017-00189-0
They report a PMF with the total reaction, but say this is not quantitative and report the individual stages of the transition separate as the quantitative part.
Good luck,
Pim
In the ideal case where you really sampled the complete space you have the true state free energies, so then you can just manually add the PMFs together if you use the same reaction coordinate. However, you've used different residues, so this is not correct. I don't know how to do it properly, if it is possible at all.
A nice recent paper where they show an example of how to report it is this one: www.nature.com/articles/s41467-017-00189-0
They report a PMF with the total reaction, but say this is not quantitative and report the individual stages of the transition separate as the quantitative part.
Good luck,
Pim
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