Re: [AMBER] no answer so far - free energy profile for water slab

From: Carlos Simmerling <>
Date: Tue, 15 Mar 2011 07:02:44 -0400

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" <> wrote:

Hello Amber users,

I posted this question last Friday and got no answer so far. Would anyone
have any
ideas? Thanks,

-------- Original Message --------
Subject: [AMBER] free energy profile for water slab
Date: Fri, 11 Mar 2011 19:24:04 +0100
From: Martina Roeselova <>
Reply-To: AMBER Mailing List <>


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
profile along the z-axis normal to water surface. We start the umbrella
simulations with CH3Br in vacuum at a distance of 10 A above the slab. The
that we encountered is that the WATER SLAB MOVES in the z-direction during

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
interface are added as the start point and the end point of the free energy
coordinate (50 A total distance).


o B1




o B2


We start with CH3Br at the B1 position and we restrain its motion by 2
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,
&rst iat=2596,2590,2595 r1=179.8, r2=179.9, r3=179.9, r4=180, rk2 = 10000 ,
rk3 =

(In the above, XXXRi defines the sampled window.)

We restrained the dummy atoms B1, B2 (ibelly or ntr=1).
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

&wt type='DUMPFREQ', istep1=50/
&wt type='END' /

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
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
restrained? Or any other trick?


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
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Received on Tue Mar 15 2011 - 04:30:02 PDT
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