[gmx-users] How to add water molecules one by one into the polymer system

Dallas Warren dallas.warren at monash.edu
Fri May 24 02:03:33 CEST 2019

They sound like the most appropriate method, if understanding your goal

Write your own script (your favourite, doesn't matter which language) that
uses insert-molecules, updates .top, runs grommp, runs simulation, then
repeats the cycle 500 times.

On Thu, 23 May 2019, 8:10 pm veerapandian, <veera.pandi33 at gmail.com> wrote:

> Dear Gromacs users,
> I have a polymer system and I would like to add water molecules one by one
> upto 500 water molecules.
> For instance, after adding a water molecule, I would like to
> relax/equilibrate the system for 10 ps
> and again add the molecule and perform the simulation until reaching my
> desired 500 molecules.
> Could you please help me how to approach this?
> I guess gmx insert-molecules command add the molecules at a single step
> (500 molecules in my case - Please correct me if I am wrong) but I would
> like to add periodically.
> Thanks in advance for your suggestions.
> Best regards,
> Veera
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