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On 11/12/2011 11:23 PM, Efrat Exlrod wrote:
<blockquote
cite="mid:48806A9D97E6644EB9EFA081725CE8FF50CB0D78@phoenix.ad.biu.ac.il"
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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 with
and without the -pbc nojump option.
</p>
<p> </p>
<p>For example:</p>
<p>(1) trjconv_d -s md_100ns.tpr -f md_100ns.xtc
-o md_100ns_noPBC_pbcmol.pdb -pbc mol -ur compact </p>
<p>(2) trjconv_d -s md_100ns.tpr -f md_100ns.xtc
-o md_100ns_noPBC_nojump.pdb -pbc nojump
</p>
<p> </p>
<p>With pbc=mol the solute is broken to few pieces, while the
water molecules are placed in a box with few holes. With pbc=nojump
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 and read the
'suggested trjconv 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> <br>
</p>
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</blockquote>
<br>
This is a straightforward situation where the suggested workflow
works: remove jumps (so all molecules are whole), then center on the
solute, and then put everything in some box (so -pbc mol, which
leaves the centered solute where it is).<br>
<br>
Mark<br>
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