I tried your suggestion and it seems to work.
I gave the definition of the cap directly in the topology file via tleap
"set mol cap {x y z r_cap}"
It seems to be compatible with any kind of MD even QM.
Thanks again for your help!
Best
Antoine MARION
----- Original Message -----
> Actually, it does help me a lot. You gave me a better understanding
> of those options.
> I will try to include the water cap within the topology file as you
> suggest.
> Thanks again for your help, I will let you know about any further
> tests/results.
> Best regards
> Antoine MARION
> ----- Original Message -----
> > 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
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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)
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Received on Fri Mar 14 2014 - 10:30:02 PDT
