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
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > 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 - 07:30:04 PDT
