From: Jérôme Hénin (jerome.henin_at_ibpc.fr)
Date: Fri Sep 08 2017 - 03:56:55 CDT
There is a lot of info on this online. Please look it up, then come back
with more specific questions if necessary.
Best,
Jerome
On 7 September 2017 at 21:35, Abhaysinh Gaikwad <ahgaikwa_at_aggies.ncat.edu>
wrote:
> 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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