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

Mark Abraham mark.j.abraham at gmail.com
Wed Apr 5 08:33:35 CEST 2017


On Tue, Apr 4, 2017 at 10:02 AM Jernej Zidar <jernej.zidar at gmail.com> wrote:

> 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.

As Magnus says, so long as the result honours the periodicity, which
representation is chosen is not of great importance (and readily changed
with trjconv).

> The manual lists a number of potential useful options under the switch
> "-selrpos" but the manual says nothing about what do the options do.

Ah, that could be improved. It likely relates to
and because it is common to several tools, is documented at

> How to instruct 'gmx insert-molecules' to keep the inserted molecules
> whole?

It did that already, right? :-)


> Thanks,
> Jernej
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