How can I add molecules to an equilibrated system without messing PBCs?

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GROMACS version: 2018

Hi all,

I’m doing atomistic simulations of polyisoprene with plasticizer additives to study phase behaviour. I am first equilibrating the PI which takes a long time and then I want to add the additives to the PI to observe any phase separation. The issue is that the PI is very dense and insert-molecules can’t insert the additives. If I increase the box size then there is a problem with the pbc and the simulation will explode. I have heard some people simulating with a cavity in their box where molecules can be inserted after equilibration, does anyone have any experience with this in GROMACS? Or any alternative solutions to this problem?

Thanks

2

You can use the -scale option with gmx insert-molecules. If you go very low you will then need to use alchemical FEP methods to start with downscaled interactions, which you turn on. But if a -scale 0.4 (default 0.57), or perhaps a little lower, is enough, you might manage with normal EM and equilibration.

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