Dear all,
We have recently made available a method to fix systems which were broken due to PBCs, named FixBox. Although PBCs are a standard and well-understood feature of molecular simulations, we all know how they can be an endless source of frustration, especially when automated procedures are needed. As systems became more complex over the years, we started to stumble on an increasing number of cases that could not be easily tackled with ‘trjconv -pbc cluster’ in an automated manner. Thus, we eventually developed FixBox to handle this and have been using it for quite some time as part of our constant-pH MD method. Recently we decided to publish it and make it freely available.
The method was recently presented in JCIM (https://doi.org/10.1021/acs.jcim.2c00823), and the open source software
(version 1.2) is available at In-House Software — ITQB
The software consists of a small C program. It reads as input a GRO file (single structure or trajectory) and a simple text file with some system definitions, and it does not require a topology; it generates a corresponding GRO file with the fixed system. More info can be found in the JCIM article and in the distributed README file. You may also contact us by email: cphmd@itqb.unl.pt (general in-house software) or
baptista@itqb.unl.pt.
I hope you can find FixBox useful for your work.
Best wishes,
Antonio Baptista