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

[Magnus Lundborg]

Hi,

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.

Cheers,

Magnus

Den 4 apr. 2017 10:03 skrev "Jernej Zidar" :

> 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
> --
> 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-requ...@gromacs.org.
>
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[gmx-users] gmx insert-molecules - molecules "sticking out of the box"

[Jernej Zidar]

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
-- 
Gromacs Users mailing list

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