[gmx-users] Re: trjconv for pbc

[rankinb]

Here are the steps that I used:

1.  trjconv -pbc whole -dump 37.875
2.  trjconv -pbc nojump
3.  trjconv -center
4.  g_select to make an index containing the atoms of interest
5.  trjconv to extract coordinates

Regardless of whether step 1 is used or not, the resulting coordination
shell configuration is not complete in the sense that it looks like the
figure I posted previously.  In all steps, I used the same .tpr file...is it
possible that I need to generate a new one after step 1?

Thanks,
Blake

PhD candidate
Purdue University
Ben-Amotz Lab

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