Re: Fwd: TIP4P and CHARMM27

From: Jim Phillips (
Date: Mon Nov 30 2015 - 16:21:44 CST


Could you try NAMD 2.11b1? The minimizer now enforces rigid bonds.


On Fri, 27 Nov 2015, Francesco Pietra wrote:

> 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.
> cheers
> francesco pietra
> ---------- Forwarded message ----------
> From: Francesco Pietra <>
> Date: Thu, Nov 26, 2015 at 10:50 PM
> Subject: TIP4P and CHARMM27
> To: VMD Mailing List <>
> 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

This archive was generated by hypermail 2.1.6 : Tue Dec 27 2016 - 23:21:35 CST