Hello Martina,
I'm Balazs, Milan's college :).
I read about your query in AMBER mailing list, and i think I can help you.
In NAMD I faced also to a similar problem, and I was able to solve it in NAMD.
I defined a DUMMY atom in the middle if the water box, and applied a restraint
between that dummy atom (which was fixed) and the COM of the water box.
As fair I know there is a possibility to perform umbrella sampling in NAMD ( I
never used it), but there is an alternative: ABF.
In NAMD you can use the AMBER ff as well.
If you need more help to set up such a system in NAMD, don't hesitate to
contact me :).
Hope this helps,
Balazs
> liquid/vacuum interface. The original (bulk) water box was 30 A x 30 A x 30
A. We
On Tue, 15 Mar 2011 15:57:16 +0100, Martina Roeselova wrote
> We do NVT simulation with the box elongated in one dimension (normal to the
> interface). This is a standard setup for slab simulations with liquid/vapor or
> liquid/vacuum interface. The original (bulk) water box was 30 A x 30 A x 30
A. We
> change the box size to 30 A x 30 A x 100 A, which results in a water slab of
~30 A
> thickness with two liquid/vacuum interfaces. At room temperature (T=300 K), the
> attractive interactions between water molecules are strong enough to keep them
> together as a liquid, while the volume of the box remains fixed in the NVT
run, with
> a vacuum/vapor phase region above and below the liquid slab. We do see
evaporation of
> water molecules off the surface, but the 3D periodic boundary conditions
ensure that
> an evaporated molecule is always re-captured by the opposite water surface.
>
> Martina
>
> On 15.3.2011 12:02, Carlos Simmerling wrote:
> > How are you restraining the water to stay a slab? This is not natural for a
> > vacuum water interface
> >
> > On Mar 15, 2011 3:54 AM, "Martina Roeselova"<roesel.uochb.cas.cz> wrote:
> >
> > Hello Amber users,
> >
> > I posted this question last Friday and got no answer so far. Would anyone
> > have any
> > ideas? Thanks,
> > Martina
> >
> > -------- Original Message --------
> > Subject: [AMBER] free energy profile for water slab
> > Date: Fri, 11 Mar 2011 19:24:04 +0100
> > From: Martina Roeselova<roesel.uochb.cas.cz>
> > Reply-To: AMBER Mailing List<amber.ambermd.org>
> > To: amber.ambermd.org
> >
> >
> >
> > Hi,
> >
> > we are trying to use umbrella sampling to calculate the free energy profile
> > of a
> > small molecule (CH3Br) �going through� a liquid water slab,
that is the free
> > energy
> > profile along the z-axis normal to water surface. We start the umbrella
> > sampling
> > simulations with CH3Br in vacuum at a distance of 10 A above the slab. The
> > problem
> > that we encountered is that the WATER SLAB MOVES in the z-direction during
> > the
> > simulation.
> >
> > Our system consists of one CH3Br and a slab of 863 polarizable water
> > molecules (POL3)
> > in a box (size 30 A x 30 A x 100 A). The slab is centered in the z-dim of
> > the box
> > with vacuum (vapor phase) above and below it forming two liquid/vapor
> > interfaces. Two
> > dummy atoms B1, B2 placed in the vacuum region at a distance of 10 A from
> > each
> > interface are added as the start point and the end point of the free energy
> > profile
> > coordinate (50 A total distance).
> >
> > vacuum
> >
> > o B1
> >
> > ____________________
> >
> >
> > water
> >
> > ____________________
> >
> >
> > o B2
> >
> > vacuum
> >
> >
> >
> > We start with CH3Br at the B1 position and we restrain its motion by 2
> > harmonic
> > potentials: one restraining the distance between B1 and the carbon atom of
> > CH3Br, and
> > the other restraining the angle B1-C(CH3Br)-B2. The B1-C(CH3Br) distance is
> > incremented by 1 A toward B2.
> >
> >
> > #restrains: distance from C(CH3Br)to dummy atom B1 and angle B1-C-B2
> > &rst iat=2590,2596, r1=XXXR1, r2=XXXR2, r3=XXXR3, r4=XXXR4, rk2 = 32.83, rk3
> > = 32.83,
> > &end
> > &rst iat=2596,2590,2595 r1=179.8, r2=179.9, r3=179.9, r4=180, rk2 = 10000 ,
> > rk3 =
> > 10000,&end
> >
> > (In the above, XXXRi defines the sampled window.)
> >
> >
> > We restrained the dummy atoms B1, B2 (ibelly or ntr=1).
> > &cntrl
> > imin = 0,
> > ntx = 5, irest = 1,
> > ntpr = 500, ntwr = 500, ntwx = 500,
> > iwrap = 1,
> > ntxo = 1,
> > ipol = 1,
> > ntf = 2, ntb = 1,
> > cut = 12,
> > ibelly = 0,
> > ntr = 1, restraintmask = ':865-866' , restraint_wt= 100.0
> > nstlim = 50000, dt = 0.001, t = 0,
> > ntt = 1, temp0 = 300.0, tautp = 5,
> > ntp = 0, pres0 = 1, taup = 1,
> > ntc = 2, tol = 0.00001,
> > jfastw = 0, watnam = 'PL3',
> > owtnm = 'OW', hwtnm1 = 'HW1', hwtnm2 = 'HW2',
> > nscm = 1,
> > nmropt = 1
> > &end
> >
> > /
> > &wt type='DUMPFREQ', istep1=50/
> > &wt type='END' /
> > DISANG=chi.RST_0
> > DUMPAVE=chi_vs_t_0
> >
> >
> > As mentioned above, the problem is that the water slab moves toward CH3Br
> > during the
> > run, and once CH3Br touches the water surface, it stays on the interface and
> > the
> > whole slab moves with CH3Br along the B1-B2 line. The control of the center
> > of mass
> > motion (nscm=1) does not work with ibelly=1 nor ntr=1. One would like to
> > keep the COM
> > of the water slab frozen to prevent the water slab from moving, but
> > apparently the
> > maximum number of atoms that can be restrained like this is 200, while our
> > slab has
> > over 800 water molecules. Can anyone advise us how to keep COM of the water
> > slab
> > restrained? Or any other trick?
> >
> > Thanks.
> > Martina
> >
> >
> > --
> > Dr. Martina Roeselova
> > Center for Biomolecules and Complex Molecular Systems
> > Institute of Organic Chemistry and Biochemistry
> > Academy of Sciences of the Czech Republic
> > Flemingovo nam. 2
> > 166 10 Prague 6
> > Czech Republic
> > www.molecular.cz/~roesel
> >
> >
> > _______________________________________________
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> >
> >
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> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
> --
> Dr. Martina Roeselova
> Center for Biomolecules and Complex Molecular Systems
> Institute of Organic Chemistry and Biochemistry
> Academy of Sciences of the Czech Republic
> Flemingovo nam. 2
> 166 10 Prague 6
> Czech Republic
>
> tel: +420-220 410 313
> fax: +420-220 410 320
> secretary: +420-220 410 321
>
> martina.roeselova.uochb.cas.cz
> www.molecular.cz/~roesel
>
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Received on Wed Mar 16 2011 - 08:00:05 PDT
