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marrink-lab / polyply_1.0

Generate input parameters and coordinates for atomistic and coarse-grained simulations of polymers, ssDNA, and carbohydrates
Apache License 2.0
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Unclear Section - Tutorial: GROMOS Polymer Melts #352

Closed saabirpetker closed 6 months ago

saabirpetker commented 7 months ago

Unclear what the "-DEQ_polyply" flag is, as mentioned at the end of section 4.

fgrunewald commented 7 months ago

it's a GROMACS define statement; you have to include it at the top of the MDP file to activate the polyply-specific bonded interactions required for relaxation. 

define = -Deq_polyply

also see https://manual.gromacs.org/documentation/current/user-guide/mdp-options.html