Re: Constraining and imparting motion to a geometry

From: Abhaysinh Gaikwad (ahgaikwa_at_aggies.ncat.edu)
Date: Thu Sep 07 2017 - 14:35:01 CDT

Hello Jerome,

Could you please explain me what exactly you mean by saying restrain a RMSD
collective variable.

Thank you,
Abhay

On Mon, Sep 4, 2017 at 8:42 AM, Jérôme Hénin <jerome.henin_at_ibpc.fr> wrote:

> Hello Abhay,
>
> The position constraints are absolute, they will conflict with a moving
> restraint such as SMD. To keep the conformation fixed, you probably want to
> restrain an *RMSD* collective variable. If you need to restrain the
> *orientation* as well, have a look at the collective variable component
> of the same name.
>
> Best,
> Jerome
>
> On 1 September 2017 at 21:47, Abhaysinh Gaikwad <ahgaikwa_at_aggies.ncat.edu>
> wrote:
>
>> Hello all,
>>
>> My system has 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. I am constraining
>> the silicon atoms to maintain their shape configuration by following
>> script.
>>
>> constraints on
>> consRef
>> consKFile
>> consKCol
>> selectConstraints on
>> selectConstrX on
>> selectConstrY on
>> selectConstrZ off
>>
>> But, before even SMD starts the silicon geometry gets break and it
>> expands. For SMD I am using following script
>>
>> SMD on
>> SMDFile
>> SMDk
>> SMDVel
>> SMDDir
>> SMDOutputFreq
>>
>> Can anyone suggest how we can maintain the silicon shape/geometry
>> constant and pull it down to the gold substrate?
>>
>> Thank you,
>> Abhay
>>
>
>

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