[gmx-users] Doubt about thermostat in MD

[Varvdekar Bhagyesh Rajendra]

Dear all,

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.



Thank you,

Bhagyesh