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pmf_of_chemicals_1-d
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| Both sides previous revisionPrevious revisionNext revision | Previous revision | ||
| pmf_of_chemicals_1-d [2018/01/31 15:25] – [WHAM for PMF] 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 | + | |
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| Here, I have 4 ETOH molecules. //ccycle// is the window number, which I named after looking through some CGUI scripts. //zmax// is the maximum distance I sample at. This will vary depending on the thickness of your system. However, you need to have points in the water because these become reference values to 0 the PMF. You may notice that there are no negative values because I assume symmetry between leaflets. Make sure to properly space apart the molecules in each window. Big molecules will need more space, so talk to Dr. Klauda if necessary. | Here, I have 4 ETOH molecules. //ccycle// is the window number, which I named after looking through some CGUI scripts. //zmax// is the maximum distance I sample at. This will vary depending on the thickness of your system. However, you need to have points in the water because these become reference values to 0 the PMF. You may notice that there are no negative values because I assume symmetry between leaflets. Make sure to properly space apart the molecules in each window. Big molecules will need more space, so talk to Dr. Klauda if necessary. | ||
| + | |||
| + | Refer to the following path in DT1 as a reference: ''/ | ||
| =====Building Systems===== | =====Building Systems===== | ||
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| 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. | ||
| - | =====Estimation of Diffusion Coefficient===== | ||
| - | //coming soon// | ||
pmf_of_chemicals_1-d.1517430329.txt.gz · Last modified: 2018/01/31 15:25 by edit