"# Learn to run simulation and implement customized coarsed-grained polymer models\n",
"# Learn to run simulation and implement customized coarsed-grained polymer models\n",
...
@@ -10,23 +10,94 @@
...
@@ -10,23 +10,94 @@
"As we've dived into the polymer objects in arbd and learned the basic usage of arbd, now it's time to put everything together and run coarsed-grained protein model using arbd! \n",
"As we've dived into the polymer objects in arbd and learned the basic usage of arbd, now it's time to put everything together and run coarsed-grained protein model using arbd! \n",
"We will constructing a polymer model by coarse-graining the HpsModel.\n",
"We will constructing a polymer model by coarse-graining the HpsModel.\n",
"\n",
"\n",
"## Step 1: Model Construction testing\n",
"## Step 1: Model Construction\n",
"\n",
"\n",
"We will begin with "
"We will start with the Hps Model we just saw in section 2 following and run the initial conformation with the same procedures. "
" damping_coefficient = 50000, # units of 1/ns\n",
" decomp_period = decomp_period,\n",
" pairlist_distance = 50+skin_depth,\n",
" dimensions = dimensions\n",
" )\n"
]
},
{
{
"cell_type": "code",
"cell_type": "code",
"execution_count": null,
"execution_count": null,
"id": "6942a0b7",
"id": "b5aef887",
"metadata": {},
"metadata": {},
"outputs": [],
"outputs": [],
"source": []
"source": []
...
...
%% Cell type:markdown id:fba6117b tags:
%% Cell type:markdown id:024005b4 tags:
# Learn to run simulation and implement customized coarsed-grained polymer models
# Learn to run simulation and implement customized coarsed-grained polymer models
As we've dived into the polymer objects in arbd and learned the basic usage of arbd, now it's time to put everything together and run coarsed-grained protein model using arbd!
As we've dived into the polymer objects in arbd and learned the basic usage of arbd, now it's time to put everything together and run coarsed-grained protein model using arbd!
We will constructing a polymer model by coarse-graining the HpsModel.
We will constructing a polymer model by coarse-graining the HpsModel.
## Step 1: Model Construction testing
## Step 1: Model Construction
We will begin with
We will start with the Hps Model we just saw in section 2 following and run the initial conformation with the same procedures.
"# Learn to run simulation and implement customized coarsed-grained polymer models\n",
"# Learn to run simulation and implement customized coarsed-grained polymer models\n",
...
@@ -10,23 +10,94 @@
...
@@ -10,23 +10,94 @@
"As we've dived into the polymer objects in arbd and learned the basic usage of arbd, now it's time to put everything together and run coarsed-grained protein model using arbd! \n",
"As we've dived into the polymer objects in arbd and learned the basic usage of arbd, now it's time to put everything together and run coarsed-grained protein model using arbd! \n",
"We will constructing a polymer model by coarse-graining the HpsModel.\n",
"We will constructing a polymer model by coarse-graining the HpsModel.\n",
"\n",
"\n",
"## Step 1: Model Construction testing\n",
"## Step 1: Model Construction\n",
"\n",
"\n",
"We will begin with "
"We will start with the Hps Model we just saw in section 2 following and run the initial conformation with the same procedures. "
" damping_coefficient = 50000, # units of 1/ns\n",
" decomp_period = decomp_period,\n",
" pairlist_distance = 50+skin_depth,\n",
" dimensions = dimensions\n",
" )\n"
]
},
{
{
"cell_type": "code",
"cell_type": "code",
"execution_count": null,
"execution_count": null,
"id": "6942a0b7",
"id": "b5aef887",
"metadata": {},
"metadata": {},
"outputs": [],
"outputs": [],
"source": []
"source": []
...
...
%% Cell type:markdown id:fba6117b tags:
%% Cell type:markdown id:024005b4 tags:
# Learn to run simulation and implement customized coarsed-grained polymer models
# Learn to run simulation and implement customized coarsed-grained polymer models
As we've dived into the polymer objects in arbd and learned the basic usage of arbd, now it's time to put everything together and run coarsed-grained protein model using arbd!
As we've dived into the polymer objects in arbd and learned the basic usage of arbd, now it's time to put everything together and run coarsed-grained protein model using arbd!
We will constructing a polymer model by coarse-graining the HpsModel.
We will constructing a polymer model by coarse-graining the HpsModel.
## Step 1: Model Construction testing
## Step 1: Model Construction
We will begin with
We will start with the Hps Model we just saw in section 2 following and run the initial conformation with the same procedures.