I want to perform Molecular simulation of amino acid ethyl ester to understand self-assembly. I will use Gromacs for this work. I want to know whether i will be able to perform simulation using Gromacs for ethyl ester. Since molecule will not be zwitterionic as carboxyl group is esterified. will that cause any problem? Which force field i should use for ester.
Rudy J Richardson
You would need to parameterize the esterified residue for the force field you are using. See the Gromacs documentation for adding a residue to a force field and modifying a force field:
http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field
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