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pmf_of_chemicals_1-d
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| pmf_of_chemicals_1-d [2018/02/01 20:22] – [PMF of Permeation for Small Molecules] edit | pmf_of_chemicals_1-d [2018/06/29 14:49] (current) – edit | ||
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| Line 6: | Line 6: | ||
| Author: Eric Wang | Author: Eric Wang | ||
| - | Please email me at // | + | Please email me at // |
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| 4. Run restrained MD\\ | 4. Run restrained MD\\ | ||
| 5. Get PMF with WHAM\\ | 5. Get PMF with WHAM\\ | ||
| - | 6. Get diffusion if you need | + | |
| Line 87: | Line 87: | ||
| Excel \\ | Excel \\ | ||
| - | 1. The bottom section of the pmf file is the energy against window number. Take this section. Using Excel, reorder the energies based on z position. Don't worry about error because you should have replicates.\\ | + | 1. The bottom section of the pmf file is the energy against window number. Take this section. Using Excel, reorder the energies based on z position.\\ |
| 2. Zero your PMF using the bulk water values. \\ | 2. Zero your PMF using the bulk water values. \\ | ||
| 3. Calculate average and standard error using replicates. If the standard error is too large, you may need to run another replicate. Make sure your PMF makes intuitive sense. Polar molecules should have high energy in the hydrophobic region, for example. | 3. Calculate average and standard error using replicates. If the standard error is too large, you may need to run another replicate. Make sure your PMF makes intuitive sense. Polar molecules should have high energy in the hydrophobic region, for example. | ||
pmf_of_chemicals_1-d.1517534520.txt.gz · Last modified: 2018/02/01 20:22 by edit