I would like to setup unrestrained MD simulations on gromacs for protein-protein complex . The protein complex was calculated by HADDOCK by using NMR Chemical shift restraints?
Could you please suggest, or give the reference to, unrestrained MD simulations?
Hello.
I think you are a little bit confused. All MD production runs are unrestrained, i.e. the atoms spatial position is allowed to move.
However, in all MD simulations, the first steps (1-10 ns) must be restrained in order to allow a correct temperature (NVT) and pressure (NPT) equilibration. Only then, the restrains can be removed and the system is allowed to equilibrate on a MD production run.
Mount your GROMACS system, do an energy minimization EM) followed by a short NVT to equilibrate pressure (10-100 ps) and a restrained NPT (2-10 ns) to allow pressure equilibration. Only after this you can remove restrains and perform an unrestricted MD run.
Check this paper: http://pubs.acs.org/doi/abs/10.1021/ct300083m.
Best regards,
Ricardo Ferreira
Unrestrained here I think refers to without artificial restraints from chemical shift. Some tutorials can be found at the GROMACS website:
http://www.gromacs.org/Documentation/Tutorials
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