[gmx-users] potential across surface again
Andre Farias de Moura
andre at qt.dq.ufscar.br
Fri Aug 6 14:55:43 CEST 2004
hi david,
I just made a series of g_potential calculations
using the most simple system available, spc216.gro
file from top dir. the potential files are in the
attachment.
(1) spc216.gro: water molecules are mostly outside
the box, potential decreases along z direction
down to 4.5 V (file potential.xvg)
(2) spc216-larger.gro: I've set z to 5.0 nm, water
molecules still outside the box, potential drops
linearly until 5.0 nm (file potential-larger.xvg),
potential doesn't match the values of (1).
(3) spc216-center.gro: I've used trjconv to center
water molecules in the box, potential now increases
along z direction (file potential-center.xvg)
(4) spc-center-larger.gro: the same structure as (3)
above but z was set to 5.0 nm, potential drops inside
water slab then jumps at the interface, but reaches
a plateau below zero (file potential-center-larger.xvg)
(5) spc216-center-larger2.gro: the same system as (4)
above but I'va used trjconv to place water molecules
in the center of the box, potential drops along water
slab, then jumps at the upper interface but attains
a negative value, lower than in (4) above (file
potential-center-larger2.xvg)
the same model system gave me five different potential
profiles although I just translated water molecules or
increased box edge length. the manual says g_potential
doesn't take periodic boundary conditions into account
but the results I got show me that pbc do matter.
I just cannot figure out what all this could mean, if
anybody can, please let me know...
thanks again
andre'
/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/
Dr. Andre' Farias de Moura
/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/
Laboratorio de Quimica Teorica
Universidade Federal de Sao Carlos
Sao Carlos - SP - Brasil
/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/
Endereco Atual
Grupo de Quimica Quantica
Instituto de Quimica de Sao Carlos
Universidade de Sao Paulo
Sao Carlos - SP - Brasil
Telefone: 55-16-3373-8055
/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/
-------------- next part --------------
# This file was created by g_potential
# which is part of G R O M A C S:
# GROwing Monsters And Cloning Shrimps
# All this happened at: Fri Aug 6 12:01:43 2004
#
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-------------- next part --------------
# This file was created by g_potential
# which is part of G R O M A C S:
# Gravel Rubs Often Many Awfully Cauterized Sores
# All this happened at: Fri Aug 6 12:03:33 2004
#
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-------------- next part --------------
# This file was created by g_potential
# which is part of G R O M A C S:
# GRoups of Organic Molecules in ACtion for Science
# All this happened at: Fri Aug 6 12:05:09 2004
#
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-------------- next part --------------
# This file was created by g_potential
# which is part of G R O M A C S:
# GROningen Mixture of Alchemy and Childrens' Stories
# All this happened at: Fri Aug 6 12:06:21 2004
#
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-------------- next part --------------
# This file was created by g_potential
# which is part of G R O M A C S:
# Giant Rising Ordinary Mutants for A Clerical Setup
# All this happened at: Fri Aug 6 12:09:06 2004
#
@ title "Electrostatic Potential"
@ xaxis label "Box (nm)"
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