VMD-L Mailing List

From: Francesco Pietra (chiendarret_at_gmail.com)
Date: Thu Nov 26 2015 - 15:50:52 CST

Hello:
For practical reasons I would like to use TIP4P water (Freddolino kit) with
CHARMM27, not 36 ff (I have params for ligands ready in the 27 ff).

Water is also a ligand at the active site (starting PDB file), and that
also should be TIP4P. Is that conceivable? Also, should TIP4P in the
solvated system be constrained as indicated in the example provided by Prof
Freddolino during minimization, NVT heating, NPT? In the final productive
NPT I would like not to constrain any bond in the protein.

In preliminary trials without constraining anything, minimization run
plainly up to ts=1.0fs; atoms moving too fast beyond that.

Thanks for advice

francesco pietra