[gmx-users] Simulation of a solid surface within Gromacs (Justin Lemkul)

Justin Lemkul jalemkul at vt.edu
Fri Nov 4 12:49:49 CET 2016

On 11/3/16 9:51 AM, Kamps, M. wrote:
> Dear Justin, GMX-users,
> First of all, thank you for the reply.
> I'm not really sure how to continue from this, there is no entry in the
> manual for either the command x2top or .n2t files. Google does provide some
> information but only limited.
> According to the information on x2top the supported input files are:
>  -f      [<.gro/.g96/...>]  (conf.gro)
>            Structure file: gro g96 pdb brk ent esp tpr
> Where should I use this n2t file, since it is not listed? I've found this
> small tutorial:
> http://chembytes.wikidot.com/grocnt , with this example n2t file:
> ; Oplsaa-based n2t for carbon-based structures such as CNTs and graphenes
> ; Andrea Minoia
> H    HJ    0.00       1.008  1    C 0.109
> ;Hydrogen
> C    CJ    0.00      12.011  3    C 0.142   H 0.109   H 0.109
> ;Periferic C
> C    CJ    0.00      12.011  3    C 0.142   C 0.142   H 0.108
> ;Periferic C
> C    CJ    0.00      12.011  1    C 0.142
> ;Internal/periodic C
> C    CJ    0.00      12.011  2    C 0.142   C 0.142
> ;Internal/periodic C
> C    CJ    0.00      12.011  3    C 0.142   C 0.142   C 0.142
> ;Internal/periodic C
> According to this file, the n2t file consists only of the molecules, its
> name, its charge, weight, number of connections, and connected atoms? Is
> this correct?

Yep, basically.  I had written a page on the .n2t file for the wiki, but it got 
nuked in the documentation overhaul and apparently there is no longer official 
documentation for the .n2t file.  I'll try to see if we can get that fixed.

> I'm kind of stuck as to how to proceed. I'm trying to implement a surface
> into gromacs. This surface is obviously inorganic and can either be
> metallic or ceramic, bonded or non-bonded. Is this possible?

If it's all held together with nonbonded interactions, then you really don't 
need to do much of anything.  Define the atom types and their parameters, and 
off you go.  The topology can be written by pdb2gmx using single-atom .rtp 
entries for the different atoms.  A bit of a hack, but should work just fine. 
Something that requires bonds and an infinite representation can only be built 
with x2top.



Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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