[gmx-users] Re: gmx-users Digest, Vol 28, Issue 16
David van der Spoel
spoel at xray.bmc.uu.se
Thu Aug 3 18:04:02 CEST 2006
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
> spoel at xray.bmc.uu.se
> <mailto:spoel at xray.bmc.uu.se> spoel at gromacs.org
> <mailto:spoel at gromacs.org> 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
>
>
> ------------------------------------------------------------------------
>
> _______________________________________________
> 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
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
--
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://folding.bmc.uu.se
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
More information about the gromacs.org_gmx-users
mailing list