Re: Steered Molecular Dynamics

From: Abhaysinh Gaikwad (
Date: Tue Aug 29 2017 - 10:25:19 CDT

Hi Bassam,

I am doing the same thing as you said but silicon geometry is breaking
during the simulation even after constraining.


On Fri, Aug 25, 2017 at 1:38 PM, Bassam Haddad <> wrote:

> Hi Abhaysinh,
> I think you should be able to constrain your silicon atoms with a hard
> spring constant, then use their collective center of mass as the anchor to
> the dummy atom that is being pulled.
> Bassam
> On Thu, Aug 24, 2017 at 11:28 AM, Abhaysinh Gaikwad <
>> wrote:
>> Hello All,
>> My system contains of two objects/geometries, one of silicon and one of
>> gold. The gold substrate is fixed at the bottom using fixed atom
>> constraints. The substrate with silicon is on the top and needs to be moved
>> to the gold atoms at a given velocity. However, the silicon atoms need to
>> maintain their shape configuration during downward movement. Can anyone
>> suggest how we can maintain the silicon shape/geometry constant and pull it
>> down to the gold substrate?

This archive was generated by hypermail 2.1.6 : Mon Dec 31 2018 - 23:20:32 CST