Dominic Rufa dominicrufa

## jnk1_solvent_lig0.ipynb

      
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                dominicrufa
                / jnk1_solvent_lig0.ipynb
            
            
              Created
              November 16, 2020 01:14
            
          
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## jnk1_solvent_lig0.ipynb
{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "This notebook attempts to yield a converged solvent-phase free energy calculation for all ligands of the jnk1 system"
   ]
  },
  {

## jnk1_solvent_lig0_revised.ipynb

      
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                dominicrufa
                / jnk1_solvent_lig0_revised.ipynb
            
            
              Created
              November 20, 2020 18:12
            
          
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## jnk1_solvent_lig0_mod2.ipynb

      
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                dominicrufa
                / jnk1_solvent_lig0_mod2.ipynb
            
            
              Created
              November 20, 2020 20:19
            
          
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## jnk1_solvent_lig0_eq8_incl
{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "This notebook attempts to yield a converged solvent-phase free energy calculation for all ligands of the jnk1 system"
   ]
  },
  {

## mod_jnk1.ipynb

      
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                dominicrufa
                / mod_jnk1.ipynb
            
            
              Created
              January 6, 2021 02:40
            
              
                added gavin's eq 8 from his notes. mod
              
          
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## openmm_torch_sandbox.ipynb

      
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                dominicrufa
                / openmm_torch_sandbox.ipynb
            
            
              Created
              April 12, 2021 19:31
            
              
                rendering failed ani_model
              
          
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## force_trouble.ipynb

      
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                dominicrufa
                / force_trouble.ipynb
            
            
              Created
              April 27, 2021 03:41
            
              
                reproducing error wherein adding a `TorchForce` to a system gives force matrices that are discrepant w.r.t. mm-only system when the scaling factor is set to zero.
              
          
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## ADP.ipynb

      
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                dominicrufa
                / ADP.ipynb
            
            
              Created
              April 29, 2021 19:57
            
              
                simpler `TorchForce` implementation on a simple vacuum dipeptide that fails in force calculation.
              
          
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## ADP_force_groups.ipynb

      
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                dominicrufa
                / ADP_force_groups.ipynb
            
            
              Created
              April 29, 2021 21:39
            
              
                placing the torchforce into force group 1 and querying the force matrices separately seems to work on a non-pbc system with `Reference` platform
              
          
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	{
	"cells": [
	{
	"cell_type": "markdown",
	"metadata": {},
	"source": [
	"This notebook attempts to yield a converged solvent-phase free energy calculation for all ligands of the jnk1 system"
	]
	},
	{