From: Jim Phillips (jim_at_ks.uiuc.edu)
Date: Mon Nov 30 2015 - 16:21:44 CST
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 <chiendarret_at_gmail.com>
> Date: Thu, Nov 26, 2015 at 10:50 PM
> Subject: TIP4P and CHARMM27
> To: VMD Mailing List <vmd-l_at_ks.uiuc.edu>
>
>
> 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
>
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