<div style="padding: 10px;">Dear gmx users <br>I have attemped to simulate a box of ethanol in normal conditions of temperature and pressure. <br>I reproduced very well
some literature data (as g(r)) however I had 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 symmetrical) peaks in 60 and 300 degrees (as
shows the figure 1 of this
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 not symmetrical) peaks the left. <br>I already made almost everything: <br>I
used both, dihedral GROMACS and Ryckaert-Bellemans, I applied almost
all the avaliables parameters <br>(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. <br>Somebody already had some experience like that? If it
had, could you give me a insight? Bellow I give my top file.<br>Thank you in advance.<br><input name="kls" value="0" type="hidden">eef
<br><input name="ienc" value="utf8" type="hidden"><br>;<br>; File 'etanol.top' was generated<br>; By user: fileti (1000)<br>; On host: linux<br>; At date: Sat Jul 15 16:41:25 2006<br>;<br>; This is your topology file
<br>; "Out Of Register Space (Ugh)" (Vi)<br>;<br>; Include forcefield parameters<br>#include "ffoplsaa.itp"<br><br>[ moleculetype ]<br>; Name nrexcl<br>ETH 2<br><br>[ atoms ]
<br>; nr type resnr residue atom cgnr charge mass typeB chargeB massB<br> 1 opls_135 1 EtOH CB 1 -0.18 12.011 ; qtot -0.18<br> 2 opls_140 1 EtOH HB1 1
0.06 1.008 ; qtot -0.12<br> 3 opls_140 1 EtOH HB2 1 0.06 1.008 ; qtot -0.06<br> 4 opls_140 1 EtOH HB3 1 0.06 1.008 ; qtot 0<br> 5 opls_157 1 EtOH CA 2
0.145 12.011 ; qtot 0.145<br> 6 opls_140 1 EtOH HA1 2 0.06 1.008 ; qtot 0.205<br> 7 opls_140 1 EtOH HA2 2 0.06 1.008 ; qtot 0.265<br> 8 opls_154 1 EtOH OH 2 -
0.683 15.9994 ; qtot -0.418<br> 9 opls_155 1 EtOH HO 2 0.418 1.008 ; qtot 0<br><br>[ bonds ]<br>; ai aj funct c0 c1 <br> 1 2 1 0.10800 284512.0
<br> 1 3 1 0.10800 284512.0<br> 1 4 1 0.10800 284512.0<br> 1 5 1 0.14040 392459.2<br> 5 6 1 0.10800 307105.6<br> 5 7 1
0.10800 307105.6<br> 5 8 1 0.13640 376560.0<br> 8 9 1 0.09450 462750.4 <br><br>[ angles ]<br>; ai aj ak funct c0 c1 <br> 2 1 3 1
107.800 276.144 <br> 2 1 4 1 107.800 276.144 <br> 2 1 5 1 107.800 276.144 <br> 3 1 4 1 107.800 276.144 <br> 3 1 5 1 110.700
313.800<br> 4 1 5 1 110.700 313.800<br> 1 5 6 1 109.500 292.880<br> 1 5 7 1 109.500 292.880<br> 1 5 8 1 109.500 418.400
<br> 6 5 7 1 107.800 276.144 <br> 6 5 8 1 115.000 334.720 <br> 7 5 8 1 108.000 585.760<br> 5 8 9 1 109.000 292.880 <br>
<br>[ dihedrals ]<br>; ai aj ak al funct c0 c1 c2 c3 c4 c5<br> 2 1 5 6 3 1.67360 -1.67360 0.00000 0.00000 0.00000 0.00000<br> 2 1 5 7 3
1.67360 -1.67360 0.00000 0.00000 0.00000 0.00000<br> 2 1 5 8 3 0.97905 2.93716 0.00000 -3.91622 0.00000 0.00000<br> 3 1 5 6 3 1.67360 -1.67360 0.00000
0.00000 0.00000 0.00000<br> 3 1 5 7 3 1.67360 -1.67360 0.00000 0.00000 0.00000 0.00000<br> 3 1 5 8 3 0.97905 2.93716 0.00000 -3.91622 0.00000
0.00000<br> 4 1 5 6 3 1.67360 -1.67360 0.00000 0.00000 0.00000 0.00000<br> 4 1 5 7 3 1.67360 -1.67360 0.00000 0.00000 0.00000 0.00000<br> 4 1 5 8 3
0.97905 2.93716 0.00000 -3.91622 0.00000 0.00000<br> 1 5 8 9 3 26.15000 -3.13800 -23.01200 0.00000 0.00000 0.00000 <br> 6 5 8 9 3 0.94140 2.82420 0.00000
-3.76560 0.00000 0.00000<br> 7 5 8 9 3 0.94140 2.82420 0.00000 -3.76560 0.00000 0.00000<br><br><br></div>______________________________________<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