[gmx-users] Re: gmx-users Digest, Vol 28, Issue 16

[Eudes Fileti]

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



> 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    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
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