From: Peter Freddolino (petefred_at_umich.edu)
Date: Fri Nov 27 2015 - 09:41:00 CST
Hi Francesco,
Could you post your config file? I’m guessing the water model or rigidbonds types are not getting recognized properly.
The warning I gave about using TIP4 with charmm force fields does not refer to the kind of error that will make your system explode, but just to the kind that will make your results questionable (arguably this is worse).
I’m confused by the description at the end of the system you’re trying to simulate. Are you using a system with all OPLSAA parameters, or mixing an OPLSAA molecule with other molecules that have charmm parameters (eg, charmm27 protein)? The latter should not be done.
Best,
Peter
> On Nov 27, 2015, at 10:17 AM, Francesco Pietra <chiendarret_at_gmail.com> 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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