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

From: Martina Roeselova <roesel.uochb.cas.cz>
Date: Tue, 15 Mar 2011 10:20:09 +0100

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 <roesel.uochb.cas.cz>
Reply-To: AMBER Mailing List <amber.ambermd.org>
To: amber.ambermd.org


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

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).


o B1




o B2


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,
&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 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?


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 - 02:00:02 PDT
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