Hello, I am a beginner in GROMACS and I am using GROMACS to analyse the solution structure of protein in water after initial homology/abinitio modelling. I have already run a search on the gmx_users list for my queries. There are a few basic questions i would like to ask.
1. In the md integrator, what is the total simulation time used in simulation of peptides in general? I'm currently using 200ps, consisting of nsteps=100000, and dt=0.002 and the rmsd graph has not reached a plateau region still. 2. Is minimisation in GROMACS only used as a precursor to the md-simulation to remove bad contacts, or can we also use it effectively to minimize a raw modelled ab-initio structure.? any help would be greatly appreciated. Thanking you, yours sincerely, Priya Chandran Dept. of Physics Indian Institute of Science
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