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

[Mark Abraham]

Hi,

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
http://manual.gromacs.org/documentation/2016/user-guide/cmdline.html#gmx-insert-molecules,
and because it is common to several tools, is documented at
http://manual.gromacs.org/documentation/2016/onlinehelp/selections.html#specifying-selections-from-command-line
.


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

It did that already, right? :-)

Mark


> Thanks,
> Jernej
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