extra bits

Author: IAlibay

rules/ligand_fep.smk

@@ -90,6 +90,7 @@ rule gather_ligand_xvg:
     input:
         xvg_loc=expand("data/sims/{{ligand}}/{{run}}/ligand/fep/simulation/{state}/prod/prod.xvg",
                        state=ligand_windows)
+        # need to add gro input
     params:
         sub_loc="data/sims/{ligand}/{run}/ligand/fep/simulation",
         vdw_max_windows=3,

template/complex-equil-mdsim/README.md

@@ -0,0 +1,7 @@
+Workflow is:
+1. emin = N steps
+2. nvt_heat = 1 ns
+3. npt_equil1 = 1 ns
+4. npt_equil2 = 5 ns
+5. npt_prod1 = 20 ns
+6. boreschcalc using npt_prod1

template/ligand-equil-mdsim/README.md

@@ -1 +1,7 @@
 Cutoffs were set to 1.0 nm in order to reflect our FEP simulations
+
+Workflow is:
+1. emin = N steps
+2. nvt_heat = 1 ns
+3. npt_equil1 = 1 ns
+4. npt_equil2 = 5 ns --> end gro file taken to ligand FEP