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--- fep [2018/01/16 12:21] – edit
+++ fep [2020/12/10 08:16] (current) – admin
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 **Free Energy Perturbation Calculation in CHARMM**
-Link to FEP files in DT2: /a/fs-3/export/home/deepthought2/aleonar2/FEP/example
+Link to FEP files in DT2:
+/lustre/jbklauda/FEP/FEP_example.zip
 To run an FEP calculation, you will need:
   - A coordinate (.crd) file for your molecule in a vacuum, equilibrated. Call it “moleculename_gas.crd,” except with your molecule’s name in the place of “moleculename.”
   - A coordinate file of your molecule in a waterbox that is an appropriate size for the molecule. Call it “moleculename_wbox.crd.” It’s important that this system is NOT equilibrated, but that the waterbox by itself IS. I have provided files for building this system if you need them, and will explain later how to use them. They can be found in the “water” folder in the “example” directory.
-  -
 Copy the files and follow these steps:
   - Check for proper permission to all .run files. Navigate to the appropriate folder in DT2. Then, you can use the "chmod" command to allow executable permission.
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   - To compute FE, you use the “total” under “final results.” Simply subtract initial from final. That is, subtract the total in the gas phase FROM the total in the water phase. Units of energy are kcal/mol.
   - Lastly, for multiple runs, be sure to change “seed” in the file “fep.run,” otherwise you will get the same exact results.
-  -
 The basic idea is that you use fep.run to submit a series of simulations of your gas and water systems separately. The file xtract.run does a WHAM analysis (see CHARMM documentation) and a thermodynamic integration analysis of the results. You subtract to find the change in FE from the gas state to the solvated state (water result – vacuum result).
 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.
-  - In the command line of DT2, you can just use CHARMM to read step4.2_waterbox.inp: charmmlink < step4.2_waterbox.inp > step4.2_waterbox.out.
+  - In the command line of DT2, you can just use CHARMM to read step4.2_waterbox.inp. Assuming the path to the CHARMM executable is "charmmlink": charmmlink < step4.2_waterbox.inp > step4.2_waterbox.out
-  - Once you have the resulting files, equilibrate the water box using step6.1_equilibration.inp: charmmlink < step6.1_equilibration.inp > step6.1_equilibration.out. Feel free to adjust the dynamics time if you desire. You might want to create a shell script to submit this using sbatch, as it won’t run as fast as the other steps I’m listing here.
+  - Once you have the resulting files, equilibrate the water box using step6.1_equilibration.inp: charmmlink < step6.1_equilibration.inp > step6.1_equilibration.out    Feel free to adjust the dynamics time if you desire. You might want to create a shell script to submit this using sbatch, as it won’t run as fast as the other steps I’m listing here.
   - 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/replace. NOTE that this will write the file moleculename_wbox.crd, so if you already have such a file and don’t want it deleted, you’ll want to change this.