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

[Kamps, M.]

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?

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?

Mark




On 11/1/16 8:44 AM, Kamps, M. wrote:
> Dear GMX-users,
>
> First of all, I'm sorry if my question is a stupid one. I'm pretty new to
> Gromacs and I'm trying to do my best to figure it all out.
>
> I'm trying to work with a solid surface within Gromacs. The final goal of
> my simulation is to analyse the behaviour of certain proteins on a
metallic
> or ceramic substrate and to find the energies related to this system. I'm
> having difficulties when trying to implement a surface in Gromacs.
>
> When I create a surface in, for instance, Avogadro or VMD Inorganic
> Builder, it is possible to create a .pdb file of such a structure.
However,
> none of the forcefields can handle the residues, and the error: "Residue
> 'XXX' not found in residue topology database" arises. The User Manual
gives
> several options here, but I'm not sure how to approach this problem. In
the
> manual these options are mentioned:
>
> *If you want a topology for an arbitrary molecule, you cannot use pdb2gmx
> (unless you build the .rtp entry yourself). You will have to build it by
hand,
> or use another program (such as x2top or one of the scripts contributed
by
> users to build the .top file
> *    - see if there is a different name being used for the residue in the
residue
>       database and rename as appropriate,*
> *    - parameterize the residue / molecule yourself (lots of work, even
for an
>       expert),*
> *    - find a topology file for the molecule, convert it to an .itp file
and include
>       it in your .top file,*
> *    - use another force field which has parameters available for this,*
> *    - search the primary literature for publications for parameters for
the
>       residue that are consistent with the force field that is being used*
>
> Based on the first sentence, I cannot use pdb2gmx and therefore have to
> build the topology myself. How can I do such a thing? Is there a (simple)
> guide available?
>
> Also, am I taking the right steps for creating a surface within Gromacs?
Is
> there a (easier) different way?
>

x2top is the only GROMACS tool that will be of any use here.  You will have
to
write a suitable .n2t file (see the manual) for whatever species you're
dealing
with.

-Justin