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<P>Dear users:</P>
<P> </P>
<P>In my system, I chose a triclinc box (monoclinic cell) as my periodic
boundary condition, which is defined as follows:</P>
<P> </P>
<P>editconf -f *.pdb -o -bt tric -box 5 5 10 -angles 90 90 120 -c<BR>genbox
-cp out -cs -p topol -o b4em<BR>grompp -v -f em -c b4em -p topol -o
box<BR>trjconv -f b4em -s box -o b4em2.gro -ur tric -pbc inbox </P>
<P> </P>
<P>If I used "-pbc inbox", my simulated molecule would be broken. And, if "-pbc
whole" was adapted, the molecule could be kept intact, but Gromacs told me
that has no effect for unit cell representation.</P>
<P> </P>
<P>In my simulations, I empolyed "-pbc whole" in order to keep molecule intact,
but after ~200ps simulation, mdrun is interrupted, and the initial intact
molecule is also broken at this moment. </P>
<P> </P>
<P>So, Could you tell me that the way I defined a triclinc box <STRONG>(not
hexagonal box)</STRONG> is right? </P>
<P>Which option should I choose in "trjconv" for -ur and -pbc?</P>
<P>What made my simulation stopped?</P>
<P> </P>
<P>Because this is my first time using triclinc box, many things are very
strange for me. </P>
<P>Any help is appreciated.</P>
<P> </P>
<P> </P>
<P>Xie Yinghong</P>
<P>Hong Kong University</P>
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