On Tue, 2015-03-17 at 12:54 +0200, Ibrahim Said wrote:
> Thanks for your prompt reply. I am sorry, there is some confusion because I
> am trying to solve this problem many days ago.
> My namelists for heating phase and Density equilibration phase are:
>
> #Heating up the system
>
> #First stage of equilibration
>
> &cntrl
>
> imin = 0, irest = 0, ntb = 1, ntx = 1, cut = 10, ntr = 0, ntc = 2, ntf =
> 2, tempi= 0.0, temp0 = 298.0, ntt = 3, gamma_ln = 1.0, ntp = 0,
You said your cutoff was 12 A. This puts your cutoff at 10 A. Also,
ntr=0 means you are *not* using restraints.
>
> nstlim = 10000, dt = 0.002, ntpr = 1000, ntwr = 1000, ntwx = 1000,
>
> /
>
> Keep solute fixed with weak restraint
>
> 500.0
>
> RES 1-489
There should not be a - here. The only reason you're not getting an
error, I think, is because you haven't turned restraints on.
>
> END
>
> END
>
>
> second stage
>
> #Equilibration of whole system stage 2
>
> &cntrl
>
> imin = 0, ntx = 5, irest = 1, nstlim = 250000, temp0 = 298.0, tempi =
> 298.0, ntc = 2, ntf = 2, ntt = 3, dt = 0.002,
>
> ntb = 2, ntp = 1, tautp = 1.0, taup = 1.0, ntwx = 1000, ntwr = 1000, ntpr =
> 1000, cut = 12.0, iwrap = 1, ioutfm = 1,
I would suggest against abruptly switching your cutoff. Pick one value
and be consistent your entire protocol.
>
> /
>
> The initial density was 0.2667 while the final density is 0.2838. I do not
> have any comment on these too low densities.
If your starting density is 0.2667, then your initial box was set
incorrectly. For comparison, my systems (which I solvate with tleap
instead of with packmol) have a starting density of between 0.7 and 0.8
g/mL. And tleap creates boxes that are much too big, although it is
"close enough" that constant pressure dynamics can fix it.
If your starting box density is 0.2667, you are better off recreating
your system with a more sensible box size. Note that "setBox" in tleap
assumes a rectangular box, although you made no mention of *how* you
solvated your system in packmol, and only said you used "setBox" in
tleap.
I don't think it is worth starting your simulations until you have a
starting density reasonably close to 1 g/mL (e.g., something larger than
0.7 at least). To quickly check your density, you can load your prmtop
into parmed.py and type "summary".
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Tue Mar 17 2015 - 06:30:02 PDT
