From: Francesco Pietra (
Date: Wed Dec 02 2015 - 11:47:58 CST

Continuing with namd2.11b1, which enforces rigid bonds on minimization, I
noticed a drastic behavior, as follows.

Solvating with standard TIP3P, with two of "myion" ( a special model of
ion) at the active site of my protein, "minimize", at ts=0.1fs, expelled
one of the ions out of the protein. Imposing colvars, the distance between
the two increased by 30% from 3.2 to 4.0.

In contrast, by using "run" in place of "minimize", i.e., carrying out MD
directly, without colvars (while starting with ts=0.01fs and increasing it
stepwise, the distance between the two ions was maintained.

I did not try "minimize" with namd2.10 in this case.

francesco pietra

On Tue, Dec 1, 2015 at 10:22 AM, Francesco Pietra <>

> Hi:
> Tried with NAMD_2.11b1_Linux-x86_64-multicore. Without any restraint,
> minimizations went on smoothly in three runs at ts = 0.1, 1.0, 1.5fs, 1000
> steps.
> Gradual heating (NVT) to 300K also went on smoothly in 20,000 steps,
> ts=1.5.fs.
> NPT had to be carried out at ts=1.0fs (at ts=1.5fs, it crashed at step ca
> 45,000 out of planned 100,000 with
> FATAL ERROR: High global exclusion count! (1474 vs 1473) System unstable
> or pairlistdist or cutoff too close to periodic cell size.
> RMSD reached constant values at ca half the simulation.
> Is anything that you would like to see fro the log file, or from elsewhere?
> francesco pietra
> On Mon, Nov 30, 2015 at 11:21 PM, Jim Phillips <> wrote:
>> Hi,
>> Could you try NAMD 2.11b1? The minimizer now enforces rigid bonds.
>> Jim
>> 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