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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--
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 Tue Mar 15 2011 - 08:00:04 PDT
