[gmx-users] insert-molecules module

Mark Abraham mark.j.abraham at gmail.com
Sun Feb 1 00:05:04 CET 2015

On Sat, Jan 31, 2015 at 11:24 PM, Siddhesh Kamat <canalesvcf09 at gmail.com>

> Hello everyone.
> I want to add a simple solvents in cubic box of different sizes( 2 2 2, 3 3
> 3 , etc) .I am using gmx insert-molecules command for this purpose. The
> problem I am facing is that for larger molecules(by size) it adds more
> molecules than the smaller ones for the same box size. For example: I  was
> able to add  180 molecules of MARTINI propane in a box of size 2 2 2 ,
> whereas insert-molecules command added 441 MARINI hexane for the same box
> size.

gmx insert-molecules needs to know how big things are. Check out the gmx
insert-molecules -h text for ways you might like to make useful suggestions
to it. Also, you can set an upper limit on the number of insertions if that

Also my system crashes  if I specify the box size as 5 5 5
> irrespective of solvent. Please advise and suggest possible solutions.

The tool has been rewritten for 5.1, so you might like to try that again
when we put out the first beta release shortly.


> Regards,
> Siddhesh Kamat
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