[gmx-users] Help for simulating the metalcluster

Vasilii Artyukhov darth.vasya at gmail.com
Mon Oct 1 16:06:51 CEST 2007

Sorry for advertising a competitor code on the list :) but you might want to
check out the DL_POLY package, as well...

2007/10/1, Utpal Sarkar <utpalchemiitkgp at gmail.com>:
> 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?
> 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
> I will be highly obliged if you can give me some advise regarding this.
> Thanking you in advance
> With best regards
> Utpal Sarkar
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