<p>Hi Lina,</p>
<p>Make sure to use a reference in which the molecules are together (clustered) the way you want them. </p>
<p>Cheers,</p>
<p>Tsjerk</p>
<p><blockquote type="cite">On Oct 27, 2011 11:47 AM, "lina" <<a href="mailto:lina.lastname@gmail.com">lina.lastname@gmail.com</a>> wrote:<br><br>Hi,<br>
<br>
I have a problem using<br>
<br>
trjconv_g -pbc nojump<br>
or<br>
<br>
trjconv_g -pbc nojump -center<br>
<br>
I even tried the -pbc whole.<br>
<br>
The system is protein with a small molecular, for the first time<br>
period, when I checked on pymol.<br>
they are together, but later they apart, after show cell, protein<br>
inside the cell, while this small molecular outside,<br>
<br>
I did not meet such issue before, it's used to be easy to fix the pbc<br>
problem, but not this one. a bit surprise,<br>
<br>
They are supposed to be together,<br>
<br>
Thanks for any advice,<br>
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