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.
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
Rudy J Richardson hi, for simulating self assembly of several identical proteins, If we use the Insert-molecules command in gromacs and enter the common mdp and cut-off values (for example 1.2 nm) that the force field recommends, Will the proteins that are randomly located at any distance from each other in the simulation box find each other and interact with each other to form assembled structure by molecular Dynamic?? Or should another method or software be used for self assembly of proteins??
any advice or guidance would be greatly appreciated.
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