[gmx-users] potential across surface
Andre Farias de Moura
andre at qt.dq.ufscar.br
Thu Aug 5 12:44:16 CEST 2004
hi david,
I forgot to attach the files, here it goes.
andre'
/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/
Dr. Andre' Farias de Moura
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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
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---------- Forwarded message ----------
Date: Thu, 5 Aug 2004 10:39:18 +0000 (GMT)
From: Andre Farias de Moura <andre at qt.dq.ufscar.br>
Reply-To: Discussion list for GROMACS users <gmx-users at gromacs.org>
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Subject: Re: [gmx-users] potential across surface
hi david,
I've checked both and don't think this is the problem,
the density profile shows an interfacial region less
than 0.5 nm thick and there is no overall movement.
my simulation system contains a 6.0 nm water slab in a
50 nm box (z direction), I'm sending you my potential
files to clarify what I mean. I got these files using:
g_potential -f water.xtc -s water.tpr -n index.ndx -sl 50
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
/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/
On Thu, 5 Aug 2004, David van der Spoel wrote:
> On Wed, 4 Aug 2004, Andre Farias de Moura wrote:
>
> >
> >dear gmx-users,
> >
> >I tried to use g_potential to get the potential
> >across air-water interface but I'm not sure
> >about the meaning of potential.xvg output. I
> >expected something like a nearly constant value
> >in bulk water region followed by a steep drop
> >in the interfacial region, but got instead a
> >steadly increasing function with only slight
> >changes across the interface.
> >
> >is that what g_potential should give me?
> >
> >how could I get a potential difference from
> >such plot?
>
> Have you checked how well-defined your interface is (use g_density)?
>
> Is your water slab moving? (remove center of mass motion)
> >
> >thanks in advance,
> >
> >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
> >
> >/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/
> >
> >_______________________________________________
> >gmx-users mailing list
> >gmx-users at gromacs.org
> >http://www.gromacs.org/mailman/listinfo/gmx-users
> >Please don't post (un)subscribe requests to the list. Use the
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> >
>
> --
> David.
> ________________________________________________________________________
> David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
> Dept. of Cell and Molecular Biology, Uppsala University.
> Husargatan 3, Box 596, 75124 Uppsala, Sweden
> phone: 46 18 471 4205 fax: 46 18 511 755
> spoel at xray.bmc.uu.se spoel at gromacs.org http://xray.bmc.uu.se/~spoel
> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
>
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-------------- 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: Thu Aug 5 10:15:44 2004
#
@ title "Electrostatic Potential"
@ xaxis label "Box (nm)"
@ yaxis label "Potential (V)"
@TYPE xy
@ view 0.15, 0.15, 0.75, 0.85
@ legend on
@ legend box on
@ legend loctype view
@ legend 0.78, 0.8
@ legend length 2
@ s0 legend "system"
0 -0
1 0.467793
2 1.34466
3 2.17246
4 3.02425
5 4.29521
6 5.97665
7 7.24003
8 8.0797
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10 9.75915
11 10.599
12 11.4388
13 12.2784
14 13.1178
15 13.9574
16 14.7971
17 15.6368
18 16.4766
19 17.3161
20 18.1553
21 18.9945
22 19.8339
23 20.6734
24 21.5131
25 22.3528
26 23.1924
27 24.0321
28 24.8718
29 25.7114
30 26.5511
31 27.3908
32 28.2304
33 29.0701
34 29.9098
35 30.7496
36 31.5895
37 32.4293
38 33.2693
39 34.1094
40 34.949
41 35.7885
42 36.628
43 37.4677
44 38.3075
45 39.1474
46 39.987
47 40.8265
48 41.6661
49 42.036
-------------- 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: Thu Aug 5 10:15:44 2004
#
@ title "Electric Field"
@ xaxis label "Box (nm)"
@ yaxis label "Field (V/nm)"
@TYPE xy
@ view 0.15, 0.15, 0.75, 0.85
@ legend on
@ legend box on
@ legend loctype view
@ legend 0.78, 0.8
@ legend length 2
@ s0 legend "system"
0 0
1 -9.35586e+08
2 -8.18139e+08
3 -8.37478e+08
4 -8.66096e+08
5 -1.67581e+09
6 -1.68708e+09
7 -8.3967e+08
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46 -8.3945e+08
47 -8.3945e+08
48 -8.3967e+08
49 9.98106e+07
-------------- 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: Thu Aug 5 10:15:44 2004
#
@ title "Charge Distribution"
@ xaxis label "Box (nm)"
@ yaxis label "Charge density (q/nm\S3\N)"
@TYPE xy
@ view 0.15, 0.15, 0.75, 0.85
@ legend on
@ legend box on
@ legend loctype view
@ legend 0.78, 0.8
@ legend length 2
@ s0 legend "system"
0 -0.109951
1 0.00654417
2 0.00643678
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4 0.00541118
5 -0.0949061
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45 2.43636e-05
46 2.43636e-05
47 -2.43636e-05
48 0
49 0.103837
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