VMD-L Mailing List
From: Francesco Pietra (chiendarret_at_gmail.com)
Date: Tue Dec 01 2015 - 03:22:31 CST
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
Gradual heating (NVT) to 300K also went on smoothly in 20,000 steps,
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?
On Mon, Nov 30, 2015 at 11:21 PM, Jim Phillips <jim_at_ks.uiuc.edu> wrote:
> 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
>> 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
>>> parameterization procedure. People do it, sometimes it seems to work
>>> 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.
>> 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>
>> For practical reasons I would like to use TIP4P water (Freddolino kit)
>> 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
>> 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