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Dear Mark<br><br><div><br></div><div>I used this sequence to obtain the gro file (gro reference in the next calculations)</div><div><br></div><div>g_densmap_d -f tmp-prueba.gro -n index.ndx -o tmp_prueba1.gro -princ</div><div><br></div><div><br></div><div><p class="ecxMsoNormal"><span style="font-size:9.0pt">Select a group for determining
the system size:</span></p>
<p class="ecxMsoNormal"><span style="font-size:9.0pt"> </span></p>
<p class="ecxMsoNormal"><span style="font-size:9.0pt">Group<span style=""> </span>0 (<span style="">
</span>System) has<span style=""> </span>6370 elements</span></p>
<p class="ecxMsoNormal"><span style="font-size:9.0pt"> </span></p>
<p class="ecxMsoNormal"><span style="font-size:9.0pt">Group<span style=""> </span>1 (<span style="">
</span>HEME) has<span style=""> </span>47 elements</span></p>
<p class="ecxMsoNormal"><span style="font-size:9.0pt"> </span></p>
<p class="ecxMsoNormal"><span style="font-size:9.0pt">Group<span style=""> </span>2 (<span style="">
</span>SOL) has<span style=""> </span>6321 elements</span></p>
<p class="ecxMsoNormal"><span style="font-size:9.0pt"> </span></p>
<p class="ecxMsoNormal"><span style="font-size:9.0pt">Group<span style=""> </span>3 (<span style="">
</span>NA+) has<span style=""> </span>2 elements</span></p>
<p class="ecxMsoNormal"><span style="font-size:9.0pt"> </span></p>
<p class="ecxMsoNormal"><span style="font-size:9.0pt">Group<span style=""> </span>4 (<span style=""> </span>NA) has<span style=""> </span>1 elements</span></p>
<p class="ecxMsoNormal"><span style="font-size:9.0pt"> </span></p>
<p class="ecxMsoNormal"><span style="font-size:9.0pt">Group<span style=""> </span>5 (<span style=""> </span>NC) has<span style=""> </span>1 elements</span></p>
<p class="ecxMsoNormal"><span style="font-size:9.0pt"> </span></p>
<p class="ecxMsoNormal"><span style="font-size:9.0pt">Group<span style=""> </span>6 (<span style="">
</span>CHB) has<span style=""> </span>1 elements</span></p>
<p class="ecxMsoNormal"><span style="font-size:9.0pt"> </span></p>
<p class="ecxMsoNormal"><span style="font-size:9.0pt">Group<span style=""> </span>7 (<span style="">
</span>CHD) has<span style=""> </span>1 elements</span></p>
<p class="ecxMsoNormal"><span style="font-size:9.0pt"> </span></p>
<p class="ecxMsoNormal"><span style="font-size:9.0pt">Group<span style=""> </span>8 (<span style="">
</span>CHB-CHD) has<span style=""> </span>2 elements</span></p>
<p class="ecxMsoNormal"><span style="font-size:9.0pt"> </span></p>
<p class="ecxMsoNormal"><span style="font-size:9.0pt">Group<span style=""> </span><span style=""> </span>9
(<span style=""> </span>Carb_ring) has<span style=""> </span>4 elements</span></p>
<p class="ecxMsoNormal"><span style="font-size:9.0pt"> </span></p>
<p class="ecxMsoNormal"><span style="font-size:9.0pt">Group<span style=""> </span>10 (<span style="">
</span>CHC) has<span style=""> </span>1 elements</span></p>
<p class="ecxMsoNormal"><span style="font-size:9.0pt"> </span></p>
<p class="ecxMsoNormal"><span style="font-size:9.0pt">Group<span style=""> </span>11 (<span style="">
</span>CHA) has<span style=""> </span>1 elements</span></p>
<p class="ecxMsoNormal"><span style="font-size:9.0pt"> </span></p>
<p class="ecxMsoNormal"><span style="font-size:9.0pt">Group<span style=""> </span>12 (<span style="">
</span>nitrog) has<span style=""> </span>3 elements</span></p>
<p class="ecxMsoNormal"><span style="font-size:9.0pt"> </span></p>
<p class="ecxMsoNormal"><span style="font-size:9.0pt">Group<span style=""> </span>13 (<span style="">
</span>ow_teste) has<span style=""> </span>1 elements</span></p>
<p class="ecxMsoNormal"><span style="font-size:9.0pt"> </span></p>
<p class="ecxMsoNormal"><span style="font-size:9.0pt">Group<span style=""> </span>14 (<span style="">
</span>HW1_HW2) has<span style=""> </span>4214 elements</span></p>
<p class="ecxMsoNormal"><span style="font-size:9.0pt"> </span></p>
<p class="ecxMsoNormal"><span style="font-size:9.0pt">Group<span style=""> </span>15 (<span style=""> </span>OW) has<span style=""> </span>2107 elements</span></p>
<p class="ecxMsoNormal"><span style="font-size:9.0pt"> </span></p>
<p class="ecxMsoNormal"><span style="font-size:9.0pt">Group<span style=""> </span>16 (<span style=""> </span>Fe) has<span style=""> </span>1 elements</span></p>
<p class="ecxMsoNormal"><span style="font-size:9.0pt"> </span></p>
<p class="ecxMsoNormal"><span class="Apple-style-span" style="font-size: 12px; "> </span></p>
<p class="ecxMsoNormal"><span style="font-size:9.0pt">Select a group: 0</span></p>
<p class="ecxMsoNormal"><span style="font-size:9.0pt"> </span></p>
<p class="ecxMsoNormal"><span style="font-size:9.0pt">Selected 0: 'System'</span></p>
<p class="ecxMsoNormal"><span style="font-size:9.0pt"> </span></p>
<p class="ecxMsoNormal"><span style="font-size:9.0pt"><span style=""> </span>system size :<span style=""> </span>5.486<span style="">
</span>5.648<span style=""> </span>6.394 (nm)</span></p>
<p class="ecxMsoNormal"><span style="font-size:9.0pt"> </span></p>
<p class="ecxMsoNormal"><span style="font-size:9.0pt"><span style=""> </span>center<span style="">
</span>:<span style=""> </span>3.463<span style=""> </span>3.499<span style="">
</span>1.671 (nm)</span></p>
<p class="ecxMsoNormal"><span style="font-size:9.0pt"> </span></p>
<p class="ecxMsoNormal"><span style="font-size:9.0pt"><span style=""> </span>box vectors :<span style=""> </span>4.471<span style="">
</span>4.471<span style=""> </span>4.563 (nm)</span></p>
<p class="ecxMsoNormal"><span style="font-size:9.0pt"> </span></p>
<p class="ecxMsoNormal"><span style="font-size:9.0pt"><span style=""> </span>box angles<span style="">
</span>:<span style=""> </span>60.66<span style=""> </span>60.66<span style="">
</span>90.00 (degrees)</span></p>
<p class="ecxMsoNormal"><span style="font-size:9.0pt"> </span></p>
<p class="ecxMsoNormal"><span style="font-size:9.0pt"><span style=""> </span>box volume<span style="">
</span>:<span style=""> </span>65.78<span style=""> </span>(nm^3)</span></p>
<p class="ecxMsoNormal"><span style="font-size:9.0pt"> </span></p>
<p class="ecxMsoNormal"><span style="font-size:9.0pt"> </span></p>
<p class="ecxMsoNormal"><span style="font-size:9.0pt"> </span></p>
<p class="ecxMsoNormal"><span style="font-size:9.0pt">Select group for the
determining the orientation</span></p>
<p class="ecxMsoNormal"><span style="font-size:9.0pt"> </span></p>
<p class="ecxMsoNormal"><span style="font-size:9.0pt">Group<span style=""> </span>0 (<span style="">
</span>System) has<span style=""> </span>6370 elements</span></p>
<p class="ecxMsoNormal"><span style="font-size:9.0pt"> </span></p>
<p class="ecxMsoNormal"><span style="font-size:9.0pt">Group<span style=""> </span>1 (<span style="">
</span>HEME) has<span style=""> </span>47 elements</span></p>
<p class="ecxMsoNormal"><span style="font-size:9.0pt"> </span></p>
<p class="ecxMsoNormal"><span style="font-size:9.0pt">Group<span style=""> </span>2 (<span style="">
</span>SOL) has<span style=""> </span>6321 elements</span></p>
<p class="ecxMsoNormal"><span style="font-size:9.0pt"> </span></p>
<p class="ecxMsoNormal"><span style="font-size:9.0pt">Group<span style=""> </span>3 (<span style="">
</span>NA+) has<span style=""> </span>2 elements</span></p>
<p class="ecxMsoNormal"><span style="font-size:9.0pt"> </span></p>
<p class="ecxMsoNormal"><span style="font-size:9.0pt">Group<span style=""> </span>4 (<span style=""> </span>NA) has<span style=""> </span>1 elements</span></p>
<p class="ecxMsoNormal"><span style="font-size:9.0pt"> </span></p>
<p class="ecxMsoNormal"><span style="font-size:9.0pt">Group<span style=""> </span>5 (<span style=""> </span>NC) has<span style=""> </span>1 elements</span></p>
<p class="ecxMsoNormal"><span style="font-size:9.0pt"> </span></p>
<p class="ecxMsoNormal"><span style="font-size:9.0pt">Group<span style=""> </span>6 (<span style="">
</span>CHB) has<span style=""> </span>1 elements</span></p>
<p class="ecxMsoNormal"><span style="font-size:9.0pt"> </span></p>
<p class="ecxMsoNormal"><span style="font-size:9.0pt">Group<span style=""> </span>7 (<span style="">
</span>CHD) has<span style=""> </span>1 elements</span></p>
<p class="ecxMsoNormal"><span style="font-size:9.0pt"> </span></p>
<p class="ecxMsoNormal"><span style="font-size:9.0pt">Group<span style=""> </span>8 (<span style="">
</span>CHB-CHD) has<span style=""> </span>2 elements</span></p>
<p class="ecxMsoNormal"><span style="font-size:9.0pt"> </span></p>
<p class="ecxMsoNormal"><span style="font-size:9.0pt">Group<span style=""> </span>9 (<span style="">
</span>Carb_ring) has<span style=""> </span>4 elements</span></p>
<p class="ecxMsoNormal"><span style="font-size:9.0pt"> </span></p>
<p class="ecxMsoNormal"><span style="font-size:9.0pt">Group<span style=""> </span>10 (<span style="">
</span>CHC) has<span style=""> </span>1 elements</span></p>
<p class="ecxMsoNormal"><span style="font-size:9.0pt"> </span></p>
<p class="ecxMsoNormal"><span style="font-size:9.0pt">Group<span style=""> </span>11 (<span style="">
</span>CHA) has<span style=""> </span>1 elements</span></p>
<p class="ecxMsoNormal"><span style="font-size:9.0pt"> </span></p>
<p class="ecxMsoNormal"><span style="font-size:9.0pt">Group<span style=""> </span>12 (<span style="">
</span>nitrog) has<span style=""> </span>3 elements</span></p>
<p class="ecxMsoNormal"><span style="font-size:9.0pt"> </span></p>
<p class="ecxMsoNormal"><span style="font-size:9.0pt">Group<span style=""> </span>13 (<span style="">
</span>ow_teste) has<span style=""> </span>1 elements</span></p>
<p class="ecxMsoNormal"><span style="font-size:9.0pt"> </span></p>
<p class="ecxMsoNormal"><span style="font-size:9.0pt">Group<span style=""> </span>14 (<span style="">
</span>HW1_HW2) has<span style=""> </span>4214 elements</span></p>
<p class="ecxMsoNormal"><span style="font-size:9.0pt"> </span></p>
<p class="ecxMsoNormal"><span style="font-size:9.0pt">Group<span style=""> </span>15 (<span style=""> </span>OW) has<span style=""> </span>2107 elements</span></p>
<p class="ecxMsoNormal"><span style="font-size:9.0pt"> </span></p>
<p class="ecxMsoNormal"><span style="font-size:9.0pt">Group<span style=""> </span>16 (<span style=""> </span>Fe) has<span style=""> </span>1 elements</span></p>
<p class="ecxMsoNormal"><span style="font-size:9.0pt"> </span></p>
<p class="ecxMsoNormal"><font class="Apple-style-span" size="3"><span class="Apple-style-span" style="font-size: 12px;"><br></span></font></p>
<p class="ecxMsoNormal"><span style="font-size:9.0pt">Select a group: 8</span></p>
<p class="ecxMsoNormal"><span style="font-size:9.0pt"> </span></p>
<p class="ecxMsoNormal"><span style="font-size:9.0pt">Selected 8: 'CHB-CHD'</span></p>
<p class="ecxMsoNormal"><span style="font-size:9.0pt"> </span></p>
<p class="ecxMsoNormal"><span style="font-size:9.0pt">new system size :<span style=""> </span>5.486<span style="">
</span>5.648<span style=""> </span>6.394</span></p>
<p class="ecxMsoNormal"><span style="font-size:9.0pt"> </span></p>
<p class="ecxMsoNormal"><span style="font-size:9.0pt"><span style=""> </span>shift<span style="">
</span>: -0.110 -0.145 -0.026 (nm)</span></p>
<p class="ecxMsoNormal"><span style="font-size:9.0pt"> </span></p>
<p class="ecxMsoNormal"><span style="font-size:9.0pt">new center<span style=""> </span>:<span style="">
</span>3.353<span style=""> </span>3.353<span style=""> </span>1.645 (nm)</span></p>
<p class="ecxMsoNormal"><span style="font-size:9.0pt"> </span></p>
<p class="ecxMsoNormal"><span style="font-size:9.0pt">new box vectors :<span style=""> </span>4.471<span style="">
</span>4.471<span style=""> </span>4.563 (nm)</span></p>
<p class="ecxMsoNormal"><span style="font-size:9.0pt"> </span></p>
<p class="ecxMsoNormal"><span style="font-size:9.0pt">new box angles<span style=""> </span>:<span style="">
</span>60.66<span style=""> </span>60.66<span style=""> </span>90.00 (degrees)</span></p>
<p class="ecxMsoNormal"><span style="font-size:9.0pt"> </span></p>
<p class="ecxMsoNormal"><span style="font-size:9.0pt">new box volume<span style=""> </span>:<span style="">
</span>65.78<span style=""> </span>(nm^3)</span></p>
<p class="ecxMsoNormal"><span style="font-size:9.0pt"> </span></p>
<p class="ecxMsoNormal"><span style="font-size:9.0pt"> </span></p>
<p class="ecxMsoNormal"><span style="font-size:9.0pt"> </span></p>
<p class="ecxMsoNormal"><span style="font-size:9.0pt">Select a group for output:</span></p>
<p class="ecxMsoNormal"><span style="font-size:9.0pt"> </span></p>
<p class="ecxMsoNormal"><span style="font-size:9.0pt">Group<span style=""> </span>0 (<span style="">
</span>System) has<span style=""> </span>6370 elements</span></p>
<p class="ecxMsoNormal"><span style="font-size:9.0pt"> </span></p>
<p class="ecxMsoNormal"><span style="font-size:9.0pt">Group<span style=""> </span>1 (<span style="">
</span>HEME) has<span style=""> </span>47 elements</span></p>
<p class="ecxMsoNormal"><span style="font-size:9.0pt"> </span></p>
<p class="ecxMsoNormal"><span style="font-size:9.0pt">Group<span style=""> </span>2 (<span style="">
</span>SOL) has<span style=""> </span>6321 elements</span></p>
<p class="ecxMsoNormal"><span style="font-size:9.0pt"> </span></p>
<p class="ecxMsoNormal"><span style="font-size:9.0pt">Group<span style=""> </span>3 (<span style="">
</span>NA+) has<span style=""> </span>2 elements</span></p>
<p class="ecxMsoNormal"><span style="font-size:9.0pt"> </span></p>
<p class="ecxMsoNormal"><span style="font-size:9.0pt">Group<span style=""> </span>4 (<span style=""> </span>NA) has<span style=""> </span>1 elements</span></p>
<p class="ecxMsoNormal"><span style="font-size:9.0pt"> </span></p>
<p class="ecxMsoNormal"><span style="font-size:9.0pt">Group<span style=""> </span>5 (<span style=""> </span>NC) has<span style=""> </span>1 elements</span></p>
<p class="ecxMsoNormal"><span style="font-size:9.0pt"> </span></p>
<p class="ecxMsoNormal"><span style="font-size:9.0pt">Group<span style=""> </span>6 (<span style="">
</span>CHB) has<span style=""> </span>1 elements</span></p>
<p class="ecxMsoNormal"><span style="font-size:9.0pt"> </span></p>
<p class="ecxMsoNormal"><span style="font-size:9.0pt">Group<span style=""> </span>7 (<span style="">
</span>CHD) has<span style=""> </span>1 elements</span></p>
<p class="ecxMsoNormal"><span style="font-size:9.0pt"> </span></p>
<p class="ecxMsoNormal"><span style="font-size:9.0pt">Group<span style=""> </span>8 (<span style="">
</span>CHB-CHD) has<span style=""> </span>2 elements</span></p>
<p class="ecxMsoNormal"><span style="font-size:9.0pt"> </span></p>
<p class="ecxMsoNormal"><span style="font-size:9.0pt">Group<span style=""> </span>9 (<span style="">
</span>Carb_ring) has<span style=""> </span>4 elements</span></p>
<p class="ecxMsoNormal"><span style="font-size:9.0pt"> </span></p>
<p class="ecxMsoNormal"><span style="font-size:9.0pt">Group<span style=""> </span>10 (<span style="">
</span>CHC) has<span style=""> </span>1 elements</span></p>
<p class="ecxMsoNormal"><span style="font-size:9.0pt"> </span></p>
<p class="ecxMsoNormal"><span style="font-size:9.0pt">Group<span style=""> </span>11 (<span style="">
</span>CHA) has<span style=""> </span>1 elements</span></p>
<p class="ecxMsoNormal"><span style="font-size:9.0pt"> </span></p>
<p class="ecxMsoNormal"><span style="font-size:9.0pt">Group<span style=""> </span>12 (<span style="">
</span>nitrog) has<span style=""> </span>3 elements</span></p>
<p class="ecxMsoNormal"><span style="font-size:9.0pt"> </span></p>
<p class="ecxMsoNormal"><span style="font-size:9.0pt">Group<span style=""> </span>13 (<span style="">
</span>ow_teste) has<span style=""> </span>1 elements</span></p>
<p class="ecxMsoNormal"><span style="font-size:9.0pt"> </span></p>
<p class="ecxMsoNormal"><span style="font-size:9.0pt">Group<span style=""> </span>14 (<span style="">
</span>HW1_HW2) has<span style=""> </span>4214 elements</span></p>
<p class="ecxMsoNormal"><span style="font-size:9.0pt"> </span></p>
<p class="ecxMsoNormal"><span style="font-size:9.0pt">Group<span style=""> </span>15 (<span style=""> </span>OW) has<span style=""> </span>2107 elements</span></p>
<p class="ecxMsoNormal"><span style="font-size:9.0pt"> </span></p>
<p class="ecxMsoNormal"><span style="font-size:9.0pt">Group<span style=""> </span>16 (<span style=""> </span>Fe) has<span style=""> </span>1 elements</span></p>
<p class="ecxMsoNormal"><span style="font-size:9.0pt"> </span></p>
<p class="ecxMsoNormal"><span style="font-size:9.0pt">Select a group: 0</span></p>
<p class="ecxMsoNormal"><span style="font-size:9.0pt"> </span></p>
<p class="ecxMsoNormal"><span style="font-size:9.0pt">Selected 0: 'System'</span></p>
<p class="ecxMsoNormal"><span style="font-size:9.0pt"> </span></p><p class="ecxMsoNormal"><span style="font-size:9.0pt"><br></span></p><p class="ecxMsoNormal"><span style="font-size:9.0pt"><br></span></p><p class="ecxMsoNormal"><span class="Apple-style-span" style="font-size: 12px; ">where CHB-CHD (molecular axis) must to coincide with the axis (X or Y).</span></p><p class="ecxMsoNormal"><font class="ecxApple-style-span" size="3"><span class="ecxApple-style-span" style="font-size:12px"><br></span></font></p><p class="ecxMsoNormal"><font class="ecxApple-style-span" size="3"><span class="ecxApple-style-span" style="font-size:12px"><br></span></font></p><p class="ecxMsoNormal"><font class="ecxApple-style-span" size="3"><span class="ecxApple-style-span" style="font-size:12px">My molecule is well centered and the box axis coincide with the molecular axis (chosen according to my interest)</span></font></p><p class="ecxMsoNormal"><font class="ecxApple-style-span" size="3"><span class="ecxApple-style-span" style="font-size:12px"><br></span></font></p><p class="ecxMsoNormal"><font class="ecxApple-style-span" size="3"><span class="ecxApple-style-span" style="font-size:12px"><br></span></font></p><p class="ecxMsoNormal"><font class="ecxApple-style-span" size="3"><span class="ecxApple-style-span" style="font-size:12px">The results are similar to make it in two steps</span></font></p><p class="ecxMsoNormal"><font class="ecxApple-style-span" size="3"><span class="ecxApple-style-span" style="font-size:12px"><br></span></font></p><p class="ecxMsoNormal"><font class="ecxApple-style-span" size="3"><span class="ecxApple-style-span" style="font-size:12px"><span class="ecxApple-style-span" style="font-size:13px">(1) g_densmap_d -f tmp-prueba.gro -n index.ndx -o tmp_prueba1.gro -princ</span></span></font></p><p class="ecxMsoNormal"><font class="ecxApple-style-span" size="3"><span class="ecxApple-style-span" style="font-size:12px"><span class="ecxApple-style-span" style="font-size:13px">(2) g_densmap_d -f tmp-prueba1.gro -n index.ndx -o tmp_prueba2.gro -c</span></span></font></p><p class="ecxMsoNormal"><font class="ecxApple-style-span" size="3"><span class="ecxApple-style-span" style="font-size:12px"><span class="ecxApple-style-span" style="font-size:13px"><br></span></span></font></p><p class="ecxMsoNormal"><br></p><p class="ecxMsoNormal"><font class="ecxApple-style-span" size="3"><span class="ecxApple-style-span" style="font-size:12px"><span class="ecxApple-style-span" style="font-size:13px">The molecule was centered in every step simulation.</span></span></font></p><p class="ecxMsoNormal"><font class="ecxApple-style-span" size="3"><span class="ecxApple-style-span" style="font-size:12px"><span class="ecxApple-style-span" style="font-size:13px"><br></span></span></font></p><p class="ecxMsoNormal"><font class="ecxApple-style-span" size="3"><span class="ecxApple-style-span" style="font-size:12px"><span class="ecxApple-style-span" style="font-size:13px"><br></span></span></font></p><p class="ecxMsoNormal"><font class="ecxApple-style-span" size="3"><span class="ecxApple-style-span" style="font-size:12px"><span class="ecxApple-style-span" style="font-size:13px">trjconv_mpi_d -s heme_centered.tpr -f dm10nsheme.xtc -o dm10nsheme_cent.xtc -center -boxcenter rect -pbc mol</span></span></font></p><p class="ecxMsoNormal"><font class="ecxApple-style-span" size="3"><span class="ecxApple-style-span" style="font-size:12px"><span class="ecxApple-style-span" style="font-size:13px"><br></span></span></font></p><p class="ecxMsoNormal"><font class="ecxApple-style-span" size="3"><span class="ecxApple-style-span" style="font-size:12px"><span class="ecxApple-style-span" style="font-size:13px"><br></span></span></font></p><p class="ecxMsoNormal"><font class="ecxApple-style-span" size="3"><span class="ecxApple-style-span" style="font-size:12px"><span class="ecxApple-style-span" style="font-size:13px"><br></span></span></font></p><p class="ecxMsoNormal"><font class="ecxApple-style-span" size="3"><span class="ecxApple-style-span" style="font-size:12px"><span class="ecxApple-style-span" style="font-size:13px">The box was rotate to XY plane concide with the XY molecular plane in every step simulation</span></span></font></p><p class="ecxMsoNormal"><font class="ecxApple-style-span" size="3"><span class="ecxApple-style-span" style="font-size:12px"><span class="ecxApple-style-span" style="font-size:13px"><br></span></span></font></p><p class="ecxMsoNormal"><font class="ecxApple-style-span" size="3"><span class="ecxApple-style-span" style="font-size:12px"><span class="ecxApple-style-span" style="font-size:13px"></span></span></font></p><font class="ecxApple-style-span" size="3"><p class="ecxMsoNormal"><br></p><p class="ecxMsoNormal">trjconv_mpi_d -s tmp_prueba2.gro -f dm10nsheme_cent.xtc -o dm10nsppix_cent_norotTrans.xtc -fit rot+trans</p><p class="ecxMsoNormal"><br></p><p class="ecxMsoNormal"><br></p><p class="ecxMsoNormal"><br></p></font><BR><p class="ecxMsoNormal"><font class="ecxApple-style-span" size="3"><span class="ecxApple-style-span" style="font-size:13px">To obtain the XY density map</span></font></p><p class="ecxMsoNormal"><font class="ecxApple-style-span" size="3"><span class="ecxApple-style-span" style="font-size:13px"><br></span></font></p><p class="ecxMsoNormal"><font class="ecxApple-style-span" size="3"><span class="ecxApple-style-span" style="font-size:13px"><br></span></font></p><p class="ecxMsoNormal">g_densmap_mpi_d -f m10nsppix_cent_norotTrans.xtc -s tmp_prueba2.gro -n index.ndx -o tmpdensmaphemeXY.xpm</p><p class="ecxMsoNormal"><font class="ecxApple-style-span" size="3"><span class="ecxApple-style-span" style="font-size:13px"><br></span></font></p><p class="ecxMsoNormal"><font class="ecxApple-style-span" size="3"><span class="ecxApple-style-span" style="font-size:13px"></span></font></p><font class="ecxApple-style-span" size="3"><p class="ecxMsoNormal" style="text-indent:0in !important;margin-right:0em !important;margin-bottom:0em !important;margin-left:0em !important;padding-top:0em !important;padding-right:0em !important;padding-bottom:0em !important;padding-left:0em !important"><font class="ecxApple-style-span" size="3" style="text-indent:0in !important"><span class="ecxApple-style-span" style="text-indent:0in !important;font-size:12px"><span class="ecxApple-style-span" style="text-indent:0in !important;font-size:13px">when I applied the g_densmap tool, there is not difference with my previous result. In the density map, my molecule appear in the corner, and white diffuse regions (maybe by the box rotations) appear.</span></span></font></p><div><font class="ecxApple-style-span" size="3" style="text-indent:0in !important"><span class="ecxApple-style-span" style="text-indent:0in !important;font-size:12px"><span class="ecxApple-style-span" style="text-indent:0in !important;font-size:13px"><br></span></span></font></div></font><BR><p class="ecxMsoNormal"><font class="ecxApple-style-span" size="3"><span class="ecxApple-style-span" style="font-size:13px"><br></span></font></p><p class="ecxMsoNormal"><font class="ecxApple-style-span" size="3"><span class="ecxApple-style-span" style="font-size:13px"><br></span></font></p><p class="ecxMsoNormal"><font class="ecxApple-style-span" size="3"><span class="ecxApple-style-span" style="font-size:12px"><span class="ecxApple-style-span" style="font-size:13px">I think the problem will be the way that I eliminate the rotations and translations.</span></span></font></p><p class="ecxMsoNormal"><font class="ecxApple-style-span" size="3"><span class="ecxApple-style-span" style="font-size:12px"><span class="ecxApple-style-span" style="font-size:13px"><br></span></span></font></p><p class="ecxMsoNormal">But I don't have a <span class="ecxApple-style-span" style="line-height:25px"><span class="ecxApple-style-span" style="font-size:12pt">clear idea of what I've done wrong</span></span></p><p class="ecxMsoNormal"><br></p><p class="ecxMsoNormal"><br></p><p class="ecxMsoNormal">Regards</p><p class="ecxMsoNormal"><br></p><p class="ecxMsoNormal"><br></p><p class="ecxMsoNormal">Ricardo</p><p class="ecxMsoNormal"><font class="ecxApple-style-span" size="3"><span class="ecxApple-style-span" style="font-size:12px"><span class="ecxApple-style-span" style="font-size:13px"><br></span></span></font></p>..............................................................................................................................<div><br></div><div><p class="ecxMsoNormal"><span style="font-size:10.0pt">Please use a descriptive
subject line to help everybody.</span></p>
<p class="ecxMsoNormal"><span style="font-size:10.0pt"> </span></p>
<p class="ecxMsoNormal"><span style="font-size:10.0pt">I suspect your use editconf
is your problem. -princ may not preserve your box the way you've assumed. Try
-princ -c, or editconf -princ then editconf -c.</span></p>
<p class="ecxMsoNormal"><span style="font-size:10.0pt"> </span></p>
<p class="ecxMsoNormal"><span style="font-size:10.0pt">It's also pointless and
error-prone to compile MPI versions of the GROMACS tools. Only mdrun is
MPI-aware, and the installation guides make this clear.</span></p>
<p class="ecxMsoNormal"><span style="font-size:10.0pt"> </span></p>
<p class="ecxMsoNormal"><span style="font-size:10.0pt">Mark </span></p><p class="ecxMsoNormal"><span style="font-size:10.0pt">............................................................................................................................</span></p></div></div> <br><hr>10 000 $ de magasinage avec Hotmail. <a href="http://go.microsoft.com/?linkid=9729716">Inscrivez-vous!</a> <br /><hr />10 000 $ de magasinage avec Hotmail. <a href='http://go.microsoft.com/?linkid=9729716' target='_new'>Inscrivez-vous!</a></body>
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