Dear Dr van der Spoel<br><br>Thank you very much for your reply.<br>I made another simulation using your<br>top file and I found again the same pattern<br>for my distribution.<br><br>Could I be making some error when I m execute
<br>the
mk_angnmx and g_angle programs?<br><br>Ive been used:<br><br>mk_ndx -s topol.tpr -n angle.ndx -type ryckaert-bellemans<br><br>and at sequence<br><br>g_angle -f traj.xtc -s topol.tpr -n angle.ndx -od<br><br><br><div><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<br>Eudes Fileti wrote:<br>> Dear gmx users<br>> I have attemped to simulate a box of ethanol in normal conditions of<br>> temperature and pressure.<br>> I reproduced very well some literature data (as g(r)) however I had
<br>> problems to reproduce the angular<br>> distribution function for the dihedral (C-C-O-H).<br>> This angle must have a peak in 180 degrees and two lesser (and<br>> symmetrical) peaks in 60 and 300 degrees (as shows the figure 1 of this
<br>> link <a href="http://cbio.mskcc.org/~leonor/jpcb97.pdf">http://cbio.mskcc.org/~leonor/jpcb97.pdf</a> ).<br>> However my distribution presents a maximum in 100 degrees with two (but<br>> not symmetrical) peaks the left.
<br>> I already made almost everything:<br>> I used both, dihedral GROMACS and Ryckaert-Bellemans, I applied almost<br>> all the avaliables parameters<br>> (eg in ffoplsaabon.itp), I set nrexcl 2, 3, 4, 5, I remade the
<br>> simulation several times in with differents conditions, but always I<br>> found the same pattern.<br>> Somebody already had some experience like that? If it had, could you<br>> give me a insight? Bellow I give my top file.
<br>> Thank you in advance.<br>> eef</blockquote><div><br><br> </div><br><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">COpare to my attached one.
<br><br>--<br>David.<br>________________________________________________________________________<br>David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,<br>Dept. of Cell and Molecular Biology, Uppsala University.
<br>Husargatan 3, Box 596, 75124 Uppsala, Sweden<br>phone: 46 18 471 4205 fax: 46 18 511 755<br><a href="mailto:spoel@xray.bmc.uu.se">spoel@xray.bmc.uu.se</a> <a href="mailto:spoel@gromacs.org">spoel@gromacs.org
</a> <a href="http://folding.bmc.uu.se">http://folding.bmc.uu.se</a><br>++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++<br>-------------- next part --------------<br>;<br>; Ethanol, Jorgensen et al. JACS 118 pp. 11225 (1996)
<br>;<br>[ moleculetype ]<br>; name nrexcl<br>ETH 3<br><br>[ atoms ]<br>; nr type resnr residu atom cgnr charge mass<br> 1 opls_157 1 ETH C 1 -0.18<br> 2 opls_156 1 ETH H 1
0.06<br> 3 opls_156 1 ETH H 1 0.06<br> 4 opls_156 1 ETH H 1 0.06<br> 5 opls_157 1 ETH C 2 0.145<br> 6 opls_156 1 ETH H 2
0.06<br> 7 opls_156 1 ETH H 2 0.06<br> 8 opls_154 1 ETH OA 2 -0.683<br> 9 opls_155 1 ETH HO 2 0.418<br><br>[ bonds ]<br>; ai aj funct c0 c1
<br> 1 5 1<br> 3 1 1<br> 4 1 1<br> 2 1 1<br> 7 5 1<br> 6 5 1<br> 8 5 1<br> 9 8 1<br><br> [ pairs ]<br> ; i j func<br> 2 6
<br> 2 7<br> 2 8<br> 3 6<br> 3 7<br> 3 8<br> 4 6<br> 4 7<br> 4 8<br> 1 9<br> 6 9<br> 7 9<br><br>[ angles ]<br>; ai aj ak funct c0 c1<br>; H3<br>
2 1 5 1<br> 3 1 5 1<br> 4 1 5 1<br>;<br> 4 1 3 1<br> 4 1 2 1<br>;<br> 3 1 2 1<br>;<br> 1 5 7 1<br> 1 5 6 1
<br> 1 5 8 1<br>;<br> 5 8 9 1<br>;<br> 6 5 7 1<br> 6 5 8 1<br>;<br> 7 5 8 1<br><br>;<br>[ dihedrals ]<br> 2 1 5 8 3
<br> 3 1 5 8 3<br> 4 1 5 8 3<br> 1 5 8 9 3<br> 6 5 8 9 3<br> 7 5 8 9 3<br></blockquote></div><br>______________________________________
<br> Eudes Eterno Fileti<br> Centro de Ciência Naturais e Humanas<br> Universidade Federal do ABC<br> Rua Santa Adélia, 166
<br> CEP 09210-170<br> skype: eefileti