Writing /users/jbklauda/pub/wiki/data/cache/6/6193a558dc90ed4c190004bf67ecff70.captchaip failed
pmf_of_chemicals_1-d
Differences
This shows you the differences between two versions of the page.
| Both sides previous revisionPrevious revisionNext revision | Previous revision | ||
| pmf_of_chemicals_1-d [2018/01/31 15:24] – [WHAM for PMF] edit | pmf_of_chemicals_1-d [2018/06/29 14:49] (current) – edit | ||
|---|---|---|---|
| Line 6: | Line 6: | ||
| Author: Eric Wang | Author: Eric Wang | ||
| - | Please email me at // | + | Please email me at // |
| Line 18: | Line 18: | ||
| 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 28: | Line 28: | ||
| 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===== | ||
| Line 72: | Line 74: | ||
| Each molecule gets its own directory. For example, ETOH1 is in the e1 directory | Each molecule gets its own directory. For example, ETOH1 is in the e1 directory | ||
| + | Position time series \\ | ||
| 1. Adjust **pos*.inp**. Adjust path to psf,crd,dcd files. Adjust molecule segid if necessary. Increase mxa,mxs,mxt if necessary.\\ | 1. Adjust **pos*.inp**. Adjust path to psf,crd,dcd files. Adjust molecule segid if necessary. Increase mxa,mxs,mxt if necessary.\\ | ||
| 2. Adjust **pos*.csh**. Adjust run numbers and window range. \\ | 2. Adjust **pos*.csh**. Adjust run numbers and window range. \\ | ||
| - | 3. Submit by typing '' | + | 3. Submit by typing '' |
| The pos*.dat files are the position time series used to calculate PMF. | The pos*.dat files are the position time series used to calculate PMF. | ||
| + | WHAM \\ | ||
| 1. To do WHAM, we need a meta file. It's called **meta**. Adjust the path name to pos*.dat. Adjust the z position. Adjust the force constant (multiply by 2 because this code uses 1/2 factor). \\ | 1. To do WHAM, we need a meta file. It's called **meta**. Adjust the path name to pos*.dat. Adjust the z position. Adjust the force constant (multiply by 2 because this code uses 1/2 factor). \\ | ||
| 2. Adjust **wham.scr**. First number is minimum window (0 in mine). Second is maximum window (40 in mine). Third is # window (41). Fourth is tolerance (use .0001). Fifth is temperature. Sixth should be 0. \\ | 2. Adjust **wham.scr**. First number is minimum window (0 in mine). Second is maximum window (40 in mine). Third is # window (41). Fourth is tolerance (use .0001). Fifth is temperature. Sixth should be 0. \\ | ||
| Line 84: | 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. | ||
| - | =====Estimation of Diffusion Coefficient===== | ||
| - | //coming soon// | ||
pmf_of_chemicals_1-d.1517430280.txt.gz · Last modified: 2018/01/31 15:24 by edit