Ok, this is a little outside my area of expertise, but I think what you
actually have to do here is simulate a "real" water cap. To my
understanding what ivcap=1 does is carve some water out of bulk for
calculations, and is intended for use with PB, which as you have seen is
not supported with QM/MM. So you will have to create the water cap in
tleap, which will then be used by sander automatically (ivcap=0); you would
then use ntb=0 and igb=0 for a non-periodic simulation.
Those more experienced with QM/MM simulations may want to comment further.
Hope this helps a little,
-Dan
On Fri, Mar 14, 2014 at 8:22 AM, Antoine Marion <
antoine.marion.univ-lorraine.fr> wrote:
> Tanks for your quick answer.
>
> I have tried indeed to use the recommended settings.
>
> PB and GB works for "standard" MD, without any cap. But when I turn on the
> cap, I get a segmentation fault.
> I am actually wondering if the cap works for MD.
>
> Did I do a mistake in the cap definition?
>
> ivcap = 1
> xcap = 0.
> ycap = 0.
> zcap = 0.
> cutcap = 6.5
>
> Moreover, SEBOMD simulation requires the use of &qmmm name list, but as
> the following message says:
>
> " QMMM is not compatible with Poisson Boltzmann (igb=10 or ipb/=0)."
>
> Antoine MARION
>
> ----- Original Message -----
>
> > Hi,
>
> > MM-PBSA is a trajectory post-processing analysis method. The
> > Poisson-Boltmann implicit solvent model is used by MM-PBSA, but is
> > not
> > integral to that method. Simulations can be done with the PB implicit
> > solvent model, just as they can with the GB implicit solvent model.
> > Have
> > you tried setting the input flags as recommended by the message? Did
> > it not
> > work?
>
> > -Dan
>
> > On Fri, Mar 14, 2014 at 7:29 AM, Antoine Marion <
> > antoine.marion.univ-lorraine.fr> wrote:
>
> > > Dear Amber community,
> > >
> > > I am currently working on SEBOMD (SemiEmpirical Born-Oppenheimer
> > > Molecular
> > > Dynamics) simulations of small water clusters in gas phase at very
> > > low
> > > temperature.
> > >
> > > I was looking for a constraint that prevents my system to evaporate
> > > .
> > >
> > > The water cap procedure looks like a good candidate for this
> > > purpose
> > > (especially ivcap = 1).
> > > The problem is that this option seems to require the use of
> > > MM-PBSA.
> > >
> > > Here is the error message I get:
> > > " IVCAP == 1,5 only works with Poisson Boltzmann (igb=10 or
> > > ipb/=0)"
> > >
> > > I don't want to use MM-PBSA since, as far as I know, this method
> > > does not
> > > work for MD and has nothing to do with my purpose.
> > >
> > > Before I go deep into the code to make it work somehow, I was
> > > wondering if
> > > anyone has an idea to overcome this issue?
> > >
> > > Thanks in advance.
> > >
> > > Best regards.
> > >
> > > Antoine MARION
> > >
> > >
> > > --
> > > PhD Student
> > > SRSMC - UMR7565
> > > Université de Lorraine - CNRS
> > > Boulevard des Aiguillettes B.P. 70239
> > > F-54506 Vandoeuvre-les-Nancy, FRANCE
> > >
> > > _______________________________________________
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> > >
>
> > --
> > -------------------------
> > Daniel R. Roe, PhD
> > Department of Medicinal Chemistry
> > University of Utah
> > 30 South 2000 East, Room 201
> > Salt Lake City, UT 84112-5820
> > http://home.chpc.utah.edu/~cheatham/
> > (801) 587-9652
> > (801) 585-6208 (Fax)
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> _______________________________________________
> AMBER mailing list
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> http://lists.ambermd.org/mailman/listinfo/amber
>
--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Fri Mar 14 2014 - 09:00:05 PDT
