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<p>Hi, </p>
<p> </p>
<p>I have run simulation of a large solute in a box of water. Trying to look at the simulation output I used trjconv<a></a><a></a><a></a> with and without the -pbc<a></a><a></a><a></a> nojump<a></a><a></a><a></a> option.
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<p> </p>
<p>For example:</p>
<p>(1) trjconv_d<a></a><a></a><a></a> -s md_100ns.tpr<a></a><a></a><a></a> -f md_100ns.xtc<a></a><a></a><a></a> -o md_100ns_noPBC_pbcmol.pdb<a></a><a></a><a></a> -pbc<a></a><a></a><a></a> mol -ur<a></a><a></a><a></a> compact </p>
<p>(2) trjconv_d<a></a><a></a><a></a> -s md_100ns.tpr<a></a><a></a><a></a> -f md_100ns.xtc<a></a><a></a><a></a> -o md_100ns_noPBC_nojump.pdb<a></a><a></a><a></a> -pbc<a></a><a></a><a></a> nojump<a></a><a></a><a></a>
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<p> </p>
<p>With pbc<a></a><a></a><a></a>=mol the solute is broken to few pieces<a></a>, while the water molecules are placed in a box with few holes. With pbc<a></a><a></a><a></a>=nojump<a></a><a></a><a></a> the solute seems reasonably well but the water molecules
are scattered in a large radius around the solute, and some of them are not broken (OH or H).</p>
<p> </p>
<p>I tried many options of trjconv<a></a><a></a><a></a> and read the 'suggested trjconv<a></a><a></a><a></a> workflow' but I still can't obtain a reasonable complete system after the simulation.</p>
<p> </p>
<p>How can I solve this problem?</p>
<p> </p>
<p>Thanks, Efrat<a></a><a></a><a></a></p>
<p> </p>
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