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--- fep [2018/01/16 12:23] – edit
+++ fep [2020/12/10 08:16] (current) – admin
@@ Line 2: / Line 2: @@
 Link to FEP files in DT2:
-/a/fs-3/export/home/deepthought2/aleonar2/FEP/example
+/lustre/jbklauda/FEP/FEP_example.zip
 To run an FEP calculation, you will need:
@@ Line 22: / Line 22: @@
 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.