[gmx-users] Help for simulating the metalcluster

Mark Abraham Mark.Abraham at anu.edu.au
Mon Oct 1 16:30:39 CEST 2007

Utpal Sarkar wrote:
> Dear Gromacs Users,
>                I want to use GROMACS code to simulate the metal cluster 
> (say Iron or Na) on
> substrate (say silicon). I want to optimize the structures actually. (I 
> have optimized some metal cluster.
> using gaussian software so I know the geometry of the cluster, I mean 
> the XYZ coordinate of the atoms).
> But I want to optimized it using GROMACS. So is it possible using 
> GROMCS? If yes, then HOW?

You can do a geometry optimization. Look for tutorial material on the 
GROMACS website or http://wiki.gromacs.org here. It is likely there's no 
force field provided with GROMACS suitable for your needs, so you will 
need to consult the literature and develop suitable force field files 
with in-detail consultation of Chapter 5 of the manual. You will not be 
able to do such calculations easily if you are a newcomer to MD, GROMACS 
or computational chemistry.

> I also want to know is there any option in the code where I can 
> implement my own potential energy
> function (or force field)? (I have seen Chapter 6, Item 6.6.2, but I 
> could not able to understand whether
> is it sufficient to implement Second Moment Approximation [SMA] type 
> potential here?). 
> So is it possible to use implemet SMA type potential for metals in GROMACS?

I don't know what a SMA potential is, but GROMACS can implement 
arbitrary potential (and force) functions via table lookups. Otherwise, 
you need to hack the C code.


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