Fix mbar example (#76)

* Add requirement of mdtraj, optax and pymbar to the doc

* Fix benzen demo (#75)

* Add Gitee_mirror

* Fix mirror CI/CD

* Update ben-prm.xml

Co-authored-by: Yingze Wang <[email protected]>
Co-authored-by: Roy-Kid <[email protected]>
Co-authored-by: KuangYu <[email protected]>
Co-authored-by: Jichen Li <[email protected]>
Co-authored-by: crone <[email protected]>
Co-authored-by: Yuzhi Zhang <[email protected]>

Author: 7 people

docs/user_guide/installation.md

@@ -13,6 +13,12 @@ pip install jax==0.3.17
 ```bash
 pip install jax-md==0.2.0
 ```
++ Install [mdtraj](https://github.com/mdtraj/mdtraj), [optax](https://github.com/deepmind/optax) and [pymbar](https://github.com/choderalab/pymbar):
+```bash
+conda install -c conda-forge mdtraj==1.9.7
+pip install optax==0.1.3
+pip install pymbar==4.0.1
+```
 + Install [OpenMM](https://openmm.org/):
 ```bash
 conda install -c conda-forge openmm==7.7.0

examples/mbar/ben-prm.xml

@@ -18,11 +18,6 @@
   <HarmonicBondForce>
     <Bond type1="ca" type2="ca" length="0.24075506225207396" k="30000.0"/>
   </HarmonicBondForce>
-  <NonbondedForce coulomb14scale="0.8333333333333334" lj14scale="0.5">
-    <UseAttributeFromResidue name="charge"/>
-    <Atom type="ca" sigma="1.0" epsilon="0.0"/>
-    <Atom type="ha" sigma="1.0" epsilon="0.0"/>
-  </NonbondedForce>
   <LennardJonesForce lj14scale="0.5" useDispersionCorrection="False">
       <Atom type="ca" sigma="0.45" epsilon="1.0"/>
   </LennardJonesForce>