[gmx-users] Doubt about thermostat in MD
Varvdekar Bhagyesh Rajendra
bhagyesh.varvdekar at research.iiit.ac.in
Mon Oct 23 19:09:41 CEST 2017
I have to find vibrational spectrum of a protein-ligand complex in water using MD. Can anyone please suggest me what thermostats would be suited for NVT equilibration, NPT equilibration and MD production. I have read that for NVT, berendsen is suited while for NPT and MD part, nose-hoover is used.
Also, what constraints would be suited for finding vibrational spectrum. I plan to use all-H as constraints.
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