fep
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fep [2018/01/16 12:28] – edit | fep [2020/12/10 08:16] (current) – admin | ||
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Link to FEP files in DT2: | Link to FEP files in DT2: | ||
- | /a/fs-3/ | + | /lustre/jbklauda/FEP/FEP_example.zip |
To run an FEP calculation, | To run an FEP calculation, | ||
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On building an appropriate water box: | On building an appropriate water box: | ||
- You can use step4.2_waterbox.inp in the /water folder. Edit parameters “A,” “B,” “C,” and “watboxZ” in the file step3_size.str. Make all of these the same length, the length of your box in angstroms. Make sure your box is big enough to allow for a 7-or-so-angstrom buffer on all sides of your molecule, which should be placed centered at zero. | - You can use step4.2_waterbox.inp in the /water folder. Edit parameters “A,” “B,” “C,” and “watboxZ” in the file step3_size.str. Make all of these the same length, the length of your box in angstroms. Make sure your box is big enough to allow for a 7-or-so-angstrom buffer on all sides of your molecule, which should be placed centered at zero. | ||
- | - In the command line of DT2, you can just use CHARMM to read step4.2_waterbox.inp. Assuming the path to the CHARMM | + | - In the command line of DT2, you can just use CHARMM to read step4.2_waterbox.inp. Assuming the path to the CHARMM |
- Once you have the resulting files, equilibrate the water box using step6.1_equilibration.inp: | - Once you have the resulting files, equilibrate the water box using step6.1_equilibration.inp: | ||
- Place your molecule into the water box using step5_assembly.inp. You’ll need to change the name of your gas molecule. Mine was DMOE, so you can just use edit/ | - Place your molecule into the water box using step5_assembly.inp. You’ll need to change the name of your gas molecule. Mine was DMOE, so you can just use edit/ |
fep.1516123685.txt.gz · Last modified: 2018/01/16 12:28 by edit