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<p class="MsoNormal" style="mso-pagination:none;mso-layout-grid-align:none;
text-autospace:none"><span style="font-size:10.0pt;font-family:Arial">Dear Friends<o:p></o:p></span></p>
<p class="MsoNormal" style="mso-pagination:none;mso-layout-grid-align:none;
text-autospace:none"><span style="font-size:10.0pt;font-family:Arial"><o:p> </o:p></span></p>
<p class="MsoNormal" style="mso-pagination:none;mso-layout-grid-align:none;
text-autospace:none"><span style="font-size:10.0pt;font-family:Arial">I tried
to obtain the XY density maps of the heme using g_densmap tool.<o:p></o:p></span></p>
<p class="MsoNormal" style="mso-pagination:none;mso-layout-grid-align:none;
text-autospace:none"><span style="font-size:10.0pt;font-family:Arial"><o:p> </o:p></span></p>
<p class="MsoNormal" style="mso-pagination:none;mso-layout-grid-align:none;
text-autospace:none"><span style="font-size:10.0pt;font-family:Arial">The
molecule was centered in the box<o:p></o:p></span></p>
<p class="MsoNormal" style="mso-pagination:none;mso-layout-grid-align:none;
text-autospace:none"><span style="font-size:10.0pt;font-family:Arial">The
system was rotated to maintain the XY plane on the molecular plane.<o:p></o:p></span></p>
<p class="MsoNormal" style="mso-pagination:none;mso-layout-grid-align:none;
text-autospace:none"><span style="font-size:10.0pt;font-family:Arial">In the
reference gro file, the molecule was also centered and the plane XY was on the
molecular plane.<o:p></o:p></span></p>
<p class="MsoNormal" style="mso-pagination:none;mso-layout-grid-align:none;
text-autospace:none"><span style="font-size:10.0pt;font-family:Arial"><o:p> </o:p></span></p>
<p class="MsoNormal" style="mso-pagination:none;mso-layout-grid-align:none;
text-autospace:none"><span style="font-size:10.0pt;font-family:Arial">To create
the reference gro file<o:p></o:p></span></p>
<p class="MsoNormal" style="mso-pagination:none;mso-layout-grid-align:none;
text-autospace:none"><span style="font-size:10.0pt;font-family:Arial"><o:p> </o:p></span></p>
<p class="MsoNormal" style="mso-pagination:none;mso-layout-grid-align:none;
text-autospace:none"><span style="font-size:10.0pt;font-family:Arial">editconf_mpi_d
-f heme.gro -c -o heme_centered.gro -n index.ndx -princ<o:p></o:p></span></p>
<p class="MsoNormal" style="mso-pagination:none;mso-layout-grid-align:none;
text-autospace:none"><span style="font-size:10.0pt;font-family:Arial"><o:p> </o:p></span></p>
<p class="MsoNormal" style="mso-pagination:none;mso-layout-grid-align:none;
text-autospace:none"><span style="font-size:10.0pt;font-family:Arial"><o:p> </o:p></span></p>
<p class="MsoNormal" style="mso-pagination:none;mso-layout-grid-align:none;
text-autospace:none"><span style="font-size:10.0pt;font-family:Arial">To center
the molecule in the box<o:p></o:p></span></p>
<p class="MsoNormal" style="mso-pagination:none;mso-layout-grid-align:none;
text-autospace:none"><span style="font-size:10.0pt;font-family:Arial"><o:p> </o:p></span></p>
<p class="MsoNormal" style="mso-pagination:none;mso-layout-grid-align:none;
text-autospace:none"><span style="font-size:10.0pt;font-family:Arial">trjconv_mpi_d
-f md10ns_heme.xtc -o md10ns_heme_centered.xtc -n index.ndx -s dmpr.tpr -center
-boxcenter rect -pbc atom<o:p></o:p></span></p>
<p class="MsoNormal" style="mso-pagination:none;mso-layout-grid-align:none;
text-autospace:none"><span style="font-size:10.0pt;font-family:Arial"><o:p> </o:p></span></p>
<p class="MsoNormal" style="mso-pagination:none;mso-layout-grid-align:none;
text-autospace:none"><span style="font-size:10.0pt;font-family:Arial"><o:p> </o:p></span></p>
<p class="MsoNormal" style="mso-pagination:none;mso-layout-grid-align:none;
text-autospace:none"><span style="font-size:10.0pt;font-family:Arial">Rotations
and translations were eliminated and the XY axis on the XY molecular plane<o:p></o:p></span></p>
<p class="MsoNormal" style="mso-pagination:none;mso-layout-grid-align:none;
text-autospace:none"><span style="font-size:10.0pt;font-family:Arial"><o:p> </o:p></span></p>
<p class="MsoNormal" style="mso-pagination:none;mso-layout-grid-align:none;
text-autospace:none"><span style="font-size:10.0pt;font-family:Arial">trjconv_mpi_d
-f md10ns_heme_centered.xtc -o md10ns_heme_centrado_centered_rottrans.xtc -n
index.ndx -s heme_centered.gro -fit rot+trans<o:p></o:p></span></p>
<p class="MsoNormal" style="mso-pagination:none;mso-layout-grid-align:none;
text-autospace:none"><span style="font-size:10.0pt;font-family:Arial"><o:p> </o:p></span></p>
<p class="MsoNormal" style="mso-pagination:none;mso-layout-grid-align:none;
text-autospace:none"><span style="font-size:10.0pt;font-family:Arial">To obtain
the XY density map<o:p></o:p></span></p>
<p class="MsoNormal" style="mso-pagination:none;mso-layout-grid-align:none;
text-autospace:none"><span style="font-size:10.0pt;font-family:Arial"><o:p> </o:p></span></p>
<p class="MsoNormal" style="mso-pagination:none;mso-layout-grid-align:none;
text-autospace:none"><span style="font-size:10.0pt;font-family:Arial">g_densmap_d
-f md10ns_heme_centrado_centered_rottrans.xtc -s heme_centered.gro -n index.ndx
-o densmap.xpm <o:p></o:p></span></p>
<p class="MsoNormal" style="mso-pagination:none;mso-layout-grid-align:none;
text-autospace:none"><span style="font-size:10.0pt;font-family:Arial"><o:p> </o:p></span></p>
<p class="MsoNormal" style="mso-pagination:none;mso-layout-grid-align:none;
text-autospace:none"><span style="font-size:10.0pt;font-family:Arial"><o:p> </o:p></span></p>
<p class="MsoNormal" style="mso-pagination:none;mso-layout-grid-align:none;
text-autospace:none"><span style="font-size:10.0pt;font-family:Arial">The
result show the molecule in the corner of the figure and a diffuse withe region around the molecule.<o:p></o:p></span></p><p class="MsoNormal" style="mso-pagination:none;mso-layout-grid-align:none;
text-autospace:none"><font class="Apple-style-span" face="Arial"><br></font></p><p class="MsoNormal" style="mso-pagination:none;mso-layout-grid-align:none;
text-autospace:none"><font class="Apple-style-span" face="Arial"><br></font></p><p class="MsoNormal" style="mso-pagination:none;mso-layout-grid-align:none;
text-autospace:none"><font class="Apple-style-span" face="Arial">I will expect a more defined region around the molecule and centered.</font></p>
<p class="MsoNormal" style="mso-pagination:none;mso-layout-grid-align:none;
text-autospace:none"><span style="font-size:10.0pt;font-family:Arial"><o:p> </o:p></span></p>
<p class="MsoNormal" style="mso-pagination:none;mso-layout-grid-align:none;
text-autospace:none"><span style="font-size:10.0pt;font-family:Arial"><o:p> </o:p></span></p>
<p class="MsoNormal" style="mso-pagination:none;mso-layout-grid-align:none;
text-autospace:none"><font class="Apple-style-span" face="Arial">I need help, thanks</font></p>
<p class="MsoNormal" style="mso-pagination:none;mso-layout-grid-align:none;
text-autospace:none"><span style="font-size:10.0pt;font-family:Arial"><o:p> </o:p></span></p>
<p class="MsoNormal" style="mso-pagination:none;mso-layout-grid-align:none;
text-autospace:none"><span style="font-size:10.0pt;font-family:Arial"><o:p> </o:p></span></p>
<p class="MsoNormal" style="mso-pagination:none;mso-layout-grid-align:none;
text-autospace:none"><span style="font-size:10.0pt;font-family:Arial">Regards<o:p></o:p></span></p>
<p class="MsoNormal" style="mso-pagination:none;mso-layout-grid-align:none;
text-autospace:none"><span style="font-size:10.0pt;font-family:Arial"><o:p> </o:p></span></p>
<p class="MsoNormal" style="mso-pagination:none;mso-layout-grid-align:none;
text-autospace:none"><font class="Apple-style-span" face="Arial">Ricardo</font></p> <br /><hr />Gagnez 10 000 $ avec Hotmail! <a href='http://go.microsoft.com/?linkid=9729713' target='_new'>Participez ici</a></body>
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