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

Jernej Zidar jernej.zidar at gmail.com
Tue Apr 4 10:02:33 CEST 2017


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?


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