[gmx-users] Usage of GROMACS

Smith, Micholas D. smithmd at ornl.gov
Mon Dec 4 14:40:20 CET 2017

Hi Momin,

Unfortunately, crystalline structures are, as you have experienced, not the easiest thing to simulate using gromac's system building tools. Typically, people working on MOFs, clays, general polymers, and other non-biological systems use something like LAMMPS (or DL_Poly like you have already noted). That being said, it isn't impossible to use gromacs for these types of systems, it just takes a bit of time. 

One tool that can be useful for these types of systems with gromacs, however, is the x2top tool. It is far from perfect, but it can get you started in the right direction.


Micholas Dean Smith, PhD.
Post-doctoral Research Associate
University of Tennessee/Oak Ridge National Laboratory
Center for Molecular Biophysics

From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Momin Ahmad <momin.ahmad at kit.edu>
Sent: Monday, December 04, 2017 8:27 AM
To: gmx-users at gromacs.org
Subject: [gmx-users] Usage of GROMACS


is GROMACS meant to be used for simulations of crystaline structures
(Metal Organic Frameworks, porous materials, minerals, ...)? Almost
every paper working on MD simulations with said structures use DL_Poly
or other software. So my question would be is there a community that
uses GROMACS to simulate crystaline structures? Porting .cif files to
pdb and then trying to run pdb2gmx with writing a .rtp file is very time


Momin Ahmad

Karlsruhe Institute of Technology (KIT)
Steinbuch Centre for Computing (SCC)
Hermann-von-Helmholtz-Platz 1
76344 Eggenstein-Leopoldshafen
Phone: +49 721 608-24286
E-Mail: Momin.Ahmad at kit.edu

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