[gmx-users] editconf

[jkrieger at mrc-lmb.cam.ac.uk]

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?
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send
> a mail to gmx-users-request at gromacs.org.
>