[gmx-users] setting tc-grps and gen-vel

[qasimpars at gmail.com]

Dear users,

I am confused on the setting tc-grps, gen-vel, and continuation:

-Do you suggest one or more groups with tc-grps to simulate a protein-ligand complex? That means setting tc-grps=protein water_ions_ligand or tc-grps=system is better? And why?

-Do you think that I should set gen-vel=yes and continuation=no in the NVT, NPT and MD step? Is there any (dis)advantage of generating new velocities in all the steps?

Thanks in advance for your suggestions.