Is it possible to use Acetonitrile as solvent for Molecular Dynamics simulation in GROMACS or DESMOND?
Yes, acetonitrile can be used as a solvent in MD simulations. In GROMACS, the initial step involves parameterizing and creating a topology for acetonitrile. Subsequently, during the 'gmx solvate' step, you would solvate the system using the pre-parameterized acetonitrile to set up the solvent environment.
To run a Molecular Dynamics (MD) simulation using acetonitrile as the solvent, you can follow these general steps:
Regarding the use of acetonitrile as a solvent in GROMACS and DESMOND:
In GROMACS: GROMACS is a popular software package for MD simulations, and it is flexible enough to handle a wide range of solvents, including acetonitrile. You can use GROMACS with appropriate force field parameters for acetonitrile and set up the simulation as described above.
In DESMOND: DESMOND is a commercial MD simulation software developed by D.E. Shaw Research. While DESMOND is primarily used for explicit-solvent simulations in water, it may not have built-in parameters for acetonitrile. Therefore, it might not be as straightforward to use acetonitrile as a solvent in DESMOND compared to GROMACS, which has a more extensive range of force fields and options for custom parameterization.
Overall, GROMACS would be a more suitable choice if you specifically want to use acetonitrile as a solvent in your MD simulation due to its flexibility and support for a wide range of force fields and solvents. However, if you have access to DESMOND and would like to use acetonitrile, you may need to explore custom parameterization options or consider other solvent models supported by the software.
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