Difference between revisions of "Tinkergpu:Forcebalance"

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[http://leeping.github.io/forcebalance/doc/ForceBalance-Manual.pdf http://leeping.github.io/forcebalance/doc/ForceBalance-Manual.pdf]
[http://leeping.github.io/forcebalance/doc/ForceBalance-Manual.pdf http://leeping.github.io/forcebalance/doc/ForceBalance-Manual.pdf]


== '''Customization and parallelization for AMOEBA(+)''' ==
== '''Customization and parallelization for AMOEBA(+)''' ==
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*Tinker binding energy calculations (<code>minimize</code> and <code>analyze</code>)  
*Tinker binding energy calculations (<code>minimize</code> and <code>analyze</code>)  
*Tinker post-MD&nbsp;<code>analyze</code>&nbsp;jobs  
*Tinker post-MD&nbsp;<code>analyze</code>&nbsp;jobs  
*Tinker/Tinker-OpenMM&nbsp;<code>dynamic</code>&nbsp;jobs
*Tinker/Tinker-OpenMM&nbsp;<code>dynamic</code>&nbsp;jobs  
 
3. An extra file besides the .in is needed in order to distribute the dynamic/dynamic_omm jobs on to different Renlab cluster nodes. Specify the node filename in the .in file as
<div style="background:#eeeeee;border:1px solid #cccccc;padding:5px 10px;"><code>&nbsp;liquid_node yourfilename.node</code></div>
where the yourfilename.node should look like:
<div style="background:#eeeeee;border:1px solid #cccccc;padding:5px 10px;"><code>Liquid_Methanol &nbsp; &nbsp; &nbsp; 278.15 node78<br/> Liquid_Methanol &nbsp; &nbsp; &nbsp; 298.15 node49<br/> Liquid_Methanol &nbsp; &nbsp; &nbsp; 318.15 node79<br/> Liquid_Ethanol &nbsp; &nbsp; &nbsp; &nbsp;278.15 node83<br/> Liquid_Ethanol &nbsp; &nbsp; &nbsp; &nbsp;298.15 node73<br/> Liquid_Ethanol &nbsp; &nbsp; &nbsp; &nbsp;318.15 node55<br/> Liquid_1-Propanol &nbsp; &nbsp; 278.15 node54<br/> Liquid_1-Propanol &nbsp; &nbsp; 298.15 node47<br/> Liquid_1-Propanol &nbsp; &nbsp; 318.15 node40<br/> Liquid_2-Propanol &nbsp; &nbsp; 278.15 node44<br/> Liquid_2-Propanol &nbsp; &nbsp; 298.15 node53<br/> Liquid_2-Propanol &nbsp; &nbsp; 318.15 node85<br/> Liquid_Methane &nbsp; &nbsp; &nbsp; &nbsp; 95.15 node72<br/> Liquid_Methane &nbsp; &nbsp; &nbsp; &nbsp;105.15 node61<br/> Liquid_Ethane &nbsp; &nbsp; &nbsp; &nbsp; 154.15 node43<br/> Liquid_Ethane &nbsp; &nbsp; &nbsp; &nbsp; 174.15 node42</code></div>

Revision as of 00:10, 17 December 2020

Background

ForceBalance is an automatic parameter optimization tool that was developed by Lee-Ping Wang et al. Please read at least the following papers to understand the algorithms.

  •    J. Phys. Chem. Lett., 2014, 5 (11), pp 1885–1891 (ForceBalance paper, TIP3P and TIP4P water as examples)
  •    J. Phys. Chem. B, 2013, 117 (34), pp 9956–9972 (iAMOEBA paper)
  •    J. Phys. Chem. B, 2015, 119 (29), pp 9423–9437 (AMOEBA14 paper)

A brief tutorial on how to install, set up, and run FB is provided below.   


ForceBalance Installation

It is easy to install FB through conda tool (either Anaconda or Miniconda). For how to install conda, please go to anaconda download page (https://www.anaconda.com/products/individual).

After you have conda installed, FB can be installed through the following commands:

  conda create --name FB17 python=3.7
  conda activate FB17
  conda install --strict-channel-priority -c conda-forge forcebalance

Now ForceBalance is installed. You should be able to run (but not efficiently) FB jobs with the following setting up of inputs.


ForceBalance input files

To take amoeba water parameterization using tinker as an example, the following files are necessary to successfully run FB. 

.
├── example.in
├── forcefield
│   └── water.prm
└── targets
    ├── DimerMin
    ├── Interactions_CCSDT
    ├── Interactions_MP2
    ├── Liquid
    ├── Monomer_Moments
    ├── Monomer_Vibration
    ├── cluster-02
    ├── cluster-03

Inside the Liquid target are the input files for tinker (.key and .xyz) and experimental data (data.csv)

 Liquid/
├── data.csv
├── gas.key
├── gas.xyz
├── liquid.key
└── liquid.xyz

A cluster folder typically contains the xyz files, interactions.key and interactions.txt, which defines the QM reference and how you calculate the interaction energy for AMOEBA.

Interactions_CCSDT/
├── 01-Prism.xyz
├── 02-Cage.xyz
├── 03-Bag.xyz
├── 04-Cyclic-Chair.xyz
├── 05-Book-1.xyz
├── 06-Book-2.xyz
├── 07-Cyclic-Boat-1.xyz
├── 08-Cyclic-Boat-2.xyz
├── interactions.key
├── interactions.txt
├── monomer_exp.xyz
├── monomer_mp2.xyz
├── monomer_opt.xyz

After you setup the above files, you should be able to run ForceBalance using the simple command:

ForceBalance example.in

If ForceBalance jobs crash, check the error message and modify your setting.  More information about settings in example.in, please refer to ForceBalance manual file 

http://leeping.github.io/forcebalance/doc/ForceBalance-Manual.pdf


Customization and parallelization for AMOEBA(+)

1. Backup original FB source files

  export condaHOME = /home/liuchw/anaconda3/envs/FB17/lib/python3.7/site-packages/forcebalance
  cp $condaHOME/binding.py $condaHOME/binding.py_back
  cp $condaHOME/liquid.py $condaHOME/liquid.py_back
  cp $condaHOME/tinkerio.py $condaHOME/tinkerio.py_back
  cp $condaHOME/parser.py $condaHOME/parser.py_back
  cp $condaHOME/data/npt.py $condaHOME/data/npt.py_back

2. Download modified files and copy them to the anaconda lib directory

  git clone git@github.com:leucinw/Software-mod.git modcode
  export modfileHOME=/home/liuchw/modcode/forcebalance-1.7.5
  cp $modfileHOME/binding.py $condaHOME/binding.py
  cp $modfileHOME/liquid.py  $condaHOME/liquid.py
  cp $modfileHOME/tinkerio.py $condaHOME/tinkerio.py
  cp $modfileHOME/parser.py $condaHOME/parser.py
  cp $modfileHOME/data/npt.py $condaHOME/data/npt.py

The above customization mostly involves supports for AMOEBA+ keywords and parallelization of the serial jobs in:

  • Tinker binding energy calculations (minimize and analyze)
  • Tinker post-MD analyze jobs
  • Tinker/Tinker-OpenMM dynamic jobs

3. An extra file besides the .in is needed in order to distribute the dynamic/dynamic_omm jobs on to different Renlab cluster nodes. Specify the node filename in the .in file as

 liquid_node yourfilename.node

where the yourfilename.node should look like:

Liquid_Methanol       278.15 node78
Liquid_Methanol       298.15 node49
Liquid_Methanol       318.15 node79
Liquid_Ethanol        278.15 node83
Liquid_Ethanol        298.15 node73
Liquid_Ethanol        318.15 node55
Liquid_1-Propanol     278.15 node54
Liquid_1-Propanol     298.15 node47
Liquid_1-Propanol     318.15 node40
Liquid_2-Propanol     278.15 node44
Liquid_2-Propanol     298.15 node53
Liquid_2-Propanol     318.15 node85
Liquid_Methane         95.15 node72
Liquid_Methane        105.15 node61
Liquid_Ethane         154.15 node43
Liquid_Ethane         174.15 node42