Eudes Fileti wrote:
Dear Dr van der Spoel
Thank you very much for your reply.
I made another simulation using your
top file and I found again the same pattern
for my distribution.
Could I be making some error when I m execute
the mk_angnmx and g_angle programs?
Ive been used:
mk_ndx -s topol.tpr -n angle.ndx -type ryckaert-bellemans
and at sequence
g_angle -f traj.xtc -s topol.tpr -n angle.ndx -od
Add the flag -type ryckaert-bellemans
I get this result:
http://folding.bmc.uu.se/eth-rbdist.png
with simulations from
@Article{Wensink2003a,
author = {E. J. W. Wensink and A. C. Hoffmann and P. J. van
Maaren and D
. van der Spoel},
title = {Dynamic properties of water/alcohol mixtures
studied by computer simulation},
journal = {J. Chem. Phys.},
year = 2003,
volume = 119,
pages = {7308-7317}
}
Eudes Fileti wrote:
> Dear gmx users
> I have attemped to simulate a box of ethanol in normal conditions of
> temperature and pressure.
> I reproduced very well some literature data (as g(r)) however I had
> problems to reproduce the angular
> distribution function for the dihedral (C-C-O-H).
> This angle must have a peak in 180 degrees and two lesser (and
> symmetrical) peaks in 60 and 300 degrees (as shows the figure 1
of this
> link http://cbio.mskcc.org/~leonor/jpcb97.pdf ).
> However my distribution presents a maximum in 100 degrees with
two (but
> not symmetrical) peaks the left.
> I already made almost everything:
> I used both, dihedral GROMACS and Ryckaert-Bellemans, I applied
almost
> all the avaliables parameters
> (eg in ffoplsaabon.itp), I set nrexcl 2, 3, 4, 5, I remade the
> simulation several times in with differents conditions, but always I
> found the same pattern.
> Somebody already had some experience like that? If it had, could you
> give me a insight? Bellow I give my top file.
> Thank you in advance.
> eef
COpare to my attached one.
--
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
[EMAIL PROTECTED]
<mailto:[EMAIL PROTECTED]> [EMAIL PROTECTED]
<mailto:[EMAIL PROTECTED]> http://folding.bmc.uu.se
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
-------------- next part --------------
;
; Ethanol, Jorgensen et al. JACS 118 pp. 11225 (1996)
;
[ moleculetype ]
; name nrexcl
ETH 3
[ atoms ]
; nr type
resnr residu atom cgnr charge mass
1 opls_157 1 ETH C 1 -0.18
2 opls_156 1 ETH H 1 0.06
3 opls_156 1 ETH H 1 0.06
4 opls_156 1 ETH H 1 0.06
5 opls_157 1 ETH C 2 0.145
6 opls_156 1 ETH H 2 0.06
7 opls_156 1 ETH H 2 0.06
8 opls_154 1 ETH OA 2 -0.683
9 opls_155 1 ETH HO 2 0.418
[ bonds ]
; ai aj funct c0 c1
1 5 1
3 1 1
4 1 1
2 1 1
7 5 1
6 5 1
8 5 1
9 8 1
[ pairs ]
; i j func
2 6
2 7
2 8
3 6
3 7
3 8
4 6
4 7
4 8
1 9
6 9
7 9
[ angles ]
; ai aj ak funct c0 c1
; H3
2 1 5 1
3 1 5 1
4 1 5 1
;
4 1 3 1
4 1 2 1
;
3 1 2 1
;
1 5 7 1
1 5 6 1
1 5 8 1
;
5 8 9 1
;
6 5 7 1
6 5 8 1
;
7 5 8 1
;
[ dihedrals ]
2 1 5 8 3
3 1 5 8 3
4 1 5 8 3
1 5 8 9 3
6 5 8 9 3
7 5 8 9 3
______________________________________
Eudes Eterno Fileti
Centro de Ciência Naturais e Humanas
Universidade Federal do ABC
Rua Santa Adélia, 166
CEP 09210-170
skype: eefileti
------------------------------------------------------------------------
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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
[EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
_______________________________________________
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Please don't post (un)subscribe requests to the list. Use the
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