[gmx-users] gmx insert-molecules - molecules "sticking out of the box"

Magnus Lundborg magnus.lundborg at scilifelab.se
Tue Apr 4 10:08:47 CEST 2017


Assuming that you are using a periodic box it shouldn't matter that the
molecules are placed crossing the edges - that just means the rest will be
on the opposing side of the box when you simulate. If you wish to visualize
the system you could experiment with the -pbc options of the trjconv tool.



Den 4 apr. 2017 10:03 skrev "Jernej Zidar" <jernej.zidar at gmail.com>:

> Hi,
> I am using 'gmx insert-molecules' to insert ten rather large polymer
> molecules into a 16x16x16 nm box. The problem is that the utility inserts
> the molecules randomly (which is good) in way that leaves the polymer
> molecules sticking outside the defined box and leaving lots of space empty.
> The manual lists a number of potential useful options under the switch
> "-selrpos" but the manual says nothing about what do the options do.
> How to instruct 'gmx insert-molecules' to keep the inserted molecules
> whole?
> Thanks,
> Jernej
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