[gmx-users] Joining two simulation box into a big box

Dallas Warren dallas.warren at monash.edu
Tue Aug 28 23:27:02 CEST 2018

gmx editconf -translate

Use that to shift each box to the correct coordinate space of the
larger simulation box, by the appropriate axis dimension of each it is
being stacked on.  Join the gro files together using a text editor,
removing header and footer for intermediate boxes, adjust atom count
at top of gro file, adjust box dimensions appropriately at end of gro

Catch ya,

Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3052
dallas.warren at monash.edu
When the only tool you own is a hammer, every problem begins to resemble a nail.
On Wed, 29 Aug 2018 at 02:42, Joydeep Munshi <jom317 at lehigh.edu> wrote:
> Hello,
> I am working with polymer-fullerene bulkheterojnction layers. Currently I
> have a simulation box size of 20x20x17 nm with 3d PBC on. I have 25 of
> these simulations with different velocity seeds.
> Now I want to join them together to make a 100x100x17 nm box and then
> equillibrate the system accordingly. Following are a few questions:
> 1. How can I join them using gromacs commands and exisiting gro files??
> 2. Is this process physically/statistically reasonable ? and is it
> satatistically same if I simulate the whole process starting with a
> 100x100x17 nm box instead of joining them?
> Thank you and hope to get some answers.
> *Thanks and regards,*
> *Joydeep Munshi,*
> *Graduate Research Assistant,*
> *Packard Lab 375,*
> *Mechanical Engineering and Mechanics,*
> *Lehigh University*
> *Contact: (484)-821-6702*
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