Calculating COSMO-RS solvation free energies using COSMOtherm
Published:
This post will talk about how to calculate COSMO-RS solvation free energies using COSMOtherm program.
Posts by Tags
COSMO-RS
CUDA
Create a conda environment and use it in a no-internet machine
Published:
This post will talk about how to create a conda environment and use it in a machine without internet.
LAMMPS
Get the parameters of OPLS-AA force field and set up a MD simulation for LAMMPS
Published:
Recently some people asked me how to get the parameters of OPLS-AA force field and set up a MD simulation for LAMMPS, here’s a brief tutorial mainly using an example of 10 ns NVT simulation of the system containing 1 solute (R) and 200 methanol solvent molecules. If you have other questions after reading the post, please let me know and I can add more details.
MD simulation
Get the parameters of OPLS-AA force field and set up a MD simulation for LAMMPS
Published:
Recently some people asked me how to get the parameters of OPLS-AA force field and set up a MD simulation for LAMMPS, here’s a brief tutorial mainly using an example of 10 ns NVT simulation of the system containing 1 solute (R) and 200 methanol solvent molecules. If you have other questions after reading the post, please let me know and I can add more details.
NCI
How to make beautiful electrostatic potential maps and NCI interactions
Published:
Recently some people asked me how to make a picture of electrostatic potential map as shown in Figure 6 in my 2020 JACS paper. Although I think I could have made a more beautiful picture there… Some people are also interested in drawing the non-covalent interactions.
OPLS-AA
Get the parameters of OPLS-AA force field and set up a MD simulation for LAMMPS
Published:
Recently some people asked me how to get the parameters of OPLS-AA force field and set up a MD simulation for LAMMPS, here’s a brief tutorial mainly using an example of 10 ns NVT simulation of the system containing 1 solute (R) and 200 methanol solvent molecules. If you have other questions after reading the post, please let me know and I can add more details.
QM calculation
When should we use explicit solvent molecules in QM calculations?
Published:
Recently I have talked with several people about the use of explicit solvent molecules in QM calculations. I will summarize my personal thoughts here, it might be not fully correct, or even might be completely wrong. So any comments are welcome via the email in the left side bar.
Solvation free energy
Calculating COSMO-RS solvation free energies using COSMOtherm
Published:
This post will talk about how to calculate COSMO-RS solvation free energies using COSMOtherm program.
conda
Create a conda environment and use it in a no-internet machine
Published:
This post will talk about how to create a conda environment and use it in a machine without internet.
electrostatic potential
How to make beautiful electrostatic potential maps and NCI interactions
Published:
Recently some people asked me how to make a picture of electrostatic potential map as shown in Figure 6 in my 2020 JACS paper. Although I think I could have made a more beautiful picture there… Some people are also interested in drawing the non-covalent interactions.
explicit solvent molecules
When should we use explicit solvent molecules in QM calculations?
Published:
Recently I have talked with several people about the use of explicit solvent molecules in QM calculations. I will summarize my personal thoughts here, it might be not fully correct, or even might be completely wrong. So any comments are welcome via the email in the left side bar.
implicit solvent model
When should we use explicit solvent molecules in QM calculations?
Published:
Recently I have talked with several people about the use of explicit solvent molecules in QM calculations. I will summarize my personal thoughts here, it might be not fully correct, or even might be completely wrong. So any comments are welcome via the email in the left side bar.
pytorch
Create a conda environment and use it in a no-internet machine
Published:
This post will talk about how to create a conda environment and use it in a machine without internet.
visualization
How to make beautiful electrostatic potential maps and NCI interactions
Published:
Recently some people asked me how to make a picture of electrostatic potential map as shown in Figure 6 in my 2020 JACS paper. Although I think I could have made a more beautiful picture there… Some people are also interested in drawing the non-covalent interactions.