[gmx-users] editconf

jkrieger at mrc-lmb.cam.ac.uk jkrieger at mrc-lmb.cam.ac.uk
Mon Jan 13 18:56:53 CET 2014

In terms of cutoffs and self-interaction, this is probably fine (you have
2.2nm between copies of your peptide). In terms of aggregation this
probably too big unless you have multiple molecules in each copy.

> Dear GMX-Users,
>                       For understanding the aggregation propensity of the
> peptide I did a 1 us md simulation with periodic boundary. I defined a
> triclinic box around my peptide using editconf. The command I used is the
> following
> editconf -f tau_pep.gro -bt triclinic -d 1.1 -princ -o box.gro.
>  Here -d 1.1 make any problems in the simulation?Is the value is
> appropriate?
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