VMD-L Mailing List
From: Francesco Pietra (chiendarret_at_gmail.com)
Date: Fri Nov 27 2015 - 09:17:35 CST
Hello: Updating previous mail to VMD only. On restarting that work from
scratch, with my molecule solvated by TIP4P (Freddolino box), I was unable
to minimize the system, by any protocol of NAMD 2.10, beyond ts=0.055fs.
Both these and previous minimization at ts=1.2fs (this could not be
reproduced) did not allow heating NVT: crash at the first step from 0 to
1K, because of atoms moving too fast. All those procedure are familiar and
successful in my quarters with TIP3P. Then, I came across warnings that
unfortunately I had missed before:
Things get DICEY very fast if you try using ANY TIP4 models with charmm
> forcefields, because of how deeply the water model is baked into the charmm
> parameterization procedure. People do it, sometimes it seems to work well,
> but there's no reason to expect that it actually SHOULD give reasonable
> results. (Freddolino 29-Sep-2015, at 7:25 PM)
All my efforts above were prompted by having got a TIP4P-solvated atom
model that had been parameterized with OPLSAA in GROMACS (while I know how
to change those type of parameters to charmm27). I wonder now whether that
model was reliable work.
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