[gmx-users] Usage of GROMACS
momin.ahmad at kit.edu
Mon Dec 4 15:13:24 CET 2017
thank you for the fast reply. Unfortunately i have bad experience with
x2top and is no option for me (considering crystalline structures). I
might have to look for other options.
Am 04.12.2017 um 14:40 schrieb Smith, Micholas D.:
> 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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Karlsruhe Institute of Technology (KIT)
Steinbuch Centre for Computing (SCC)
Phone: +49 721 608-24286
E-Mail: Momin.Ahmad at kit.edu
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