[gmx-users] Problems with the Dihedral of the Ethanol
David van der Spoel
spoel at xray.bmc.uu.se
Thu Aug 3 14:09:14 CEST 2006
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
>
> ;
> ; File 'etanol.top' was generated
> ; By user: fileti (1000)
> ; On host: linux
> ; At date: Sat Jul 15 16:41:25 2006
> ;
> ; This is your topology file
> ; "Out Of Register Space (Ugh)" (Vi)
> ;
> ; Include forcefield parameters
> #include "ffoplsaa.itp"
>
> [ moleculetype ]
> ; Name nrexcl
> ETH 2
>
> [ atoms ]
> ; nr type resnr residue atom cgnr charge mass
> typeB chargeB massB
> 1 opls_135 1 EtOH CB 1 -0.18 12.011 ;
> qtot -0.18
> 2 opls_140 1 EtOH HB1 1 0.06 1.008 ;
> qtot -0.12
> 3 opls_140 1 EtOH HB2 1 0.06 1.008 ;
> qtot -0.06
> 4 opls_140 1 EtOH HB3 1 0.06 1.008 ;
> qtot 0
> 5 opls_157 1 EtOH CA 2 0.145 12.011 ;
> qtot 0.145
> 6 opls_140 1 EtOH HA1 2 0.06 1.008 ;
> qtot 0.205
> 7 opls_140 1 EtOH HA2 2 0.06 1.008 ;
> qtot 0.265
> 8 opls_154 1 EtOH OH 2 - 0.683 15.9994 ;
> qtot -0.418
> 9 opls_155 1 EtOH HO 2 0.418 1.008 ;
> qtot 0
>
> [ bonds ]
> ; ai aj funct c0 c1
> 1 2 1 0.10800 284512.0
> 1 3 1 0.10800 284512.0
> 1 4 1 0.10800 284512.0
> 1 5 1 0.14040 392459.2
> 5 6 1 0.10800 307105.6
> 5 7 1 0.10800 307105.6
> 5 8 1 0.13640 376560.0
> 8 9 1 0.09450 462750.4
>
> [ angles ]
> ; ai aj ak funct c0 c1
> 2 1 3 1 107.800 276.144
> 2 1 4 1 107.800 276.144
> 2 1 5 1 107.800 276.144
> 3 1 4 1 107.800 276.144
> 3 1 5 1 110.700 313.800
> 4 1 5 1 110.700 313.800
> 1 5 6 1 109.500 292.880
> 1 5 7 1 109.500 292.880
> 1 5 8 1 109.500 418.400
> 6 5 7 1 107.800 276.144
> 6 5 8 1 115.000 334.720
> 7 5 8 1 108.000 585.760
> 5 8 9 1 109.000 292.880
>
> [ dihedrals ]
> ; ai aj ak al funct c0 c1 c2
> c3 c4 c5
> 2 1 5 6 3 1.67360 -1.67360 0.00000
> 0.00000 0.00000 0.00000
> 2 1 5 7 3 1.67360 -1.67360 0.00000
> 0.00000 0.00000 0.00000
> 2 1 5 8 3 0.97905 2.93716 0.00000
> -3.91622 0.00000 0.00000
> 3 1 5 6 3 1.67360 -1.67360 0.00000
> 0.00000 0.00000 0.00000
> 3 1 5 7 3 1.67360 -1.67360 0.00000
> 0.00000 0.00000 0.00000
> 3 1 5 8 3 0.97905 2.93716 0.00000
> -3.91622 0.00000 0.00000
> 4 1 5 6 3 1.67360 -1.67360 0.00000
> 0.00000 0.00000 0.00000
> 4 1 5 7 3 1.67360 -1.67360 0.00000
> 0.00000 0.00000 0.00000
> 4 1 5 8 3 0.97905 2.93716 0.00000
> -3.91622 0.00000 0.00000
> 1 5 8 9 3 26.15000 -3.13800 -23.01200
> 0.00000 0.00000 0.00000
> 6 5 8 9 3 0.94140 2.82420 0.00000
> -3.76560 0.00000 0.00000
> 7 5 8 9 3 0.94140 2.82420 0.00000
> -3.76560 0.00000 0.00000
>
>
> ______________________________________
> 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
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 --------------
An embedded and charset-unspecified text was scrubbed...
Name: eth.itp
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20060803/73698a30/attachment.ksh>
More information about the gromacs.org_gmx-users
mailing list