I am novice to the MD simulation. For MD simulation I have been following the NAMD tutorials. In the midway I got a bit confused how should I proceed; if I have to run my simulation using Acetonitrile solvent implicitly. Because following the Generalized Born Implicit Solvent configuration file I got lost as to how to indicate the system about the specific solvent that is to be used. It would be grateful if you could help me with the script or the steps that I should follow.
to indicate specific solvent in namd is easy, insted of water you can add the solvent that you need, and provide the parameter file that include all relevent information to perform simulation. NAMD need all the parameters, therefore, for a new solvent you need to make or search force field for this solvent.
Thank you Tyagi Sir.
Can you please give me script file used for running implicit solvent other than water which I could use as example.
thanking you in anticipation
To incorporate new materials, you need to make force field (ff) by yourself, then you need to show this in the configuration file, their is a specific part belong to "parameter on" below this you need to put your file.
For example try using VMD tool kit for FFTK, this will help you to make a ff for acetonitrile. Or you may try to use online avilable CGENFF webpage to design ff for smaller molecule.
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