[CP2K-user] Steered Molecular Dynamics

Dev Rana dev.... at gmail.com
Mon Nov 2 14:30:19 UTC 2020

Hi Marcella,

Thank you for your suggestions. Is there an example of the 3rd method 
anywhere? I *think *this is the technique that I actually need. I have some 
bond lengths (RDF) from ab initio MD between different species so I'd like 
to place two atoms within the solvent. Subsequently, constraint 1 atom, and 
push the other atom toward a target distance (based on RDF). However, I'm 
not sure how to do this correctly. The closest example I have found 
is https://www.cp2k.org/exercises:2020_uzh_acpc2:ex03?s[]=target 
and https://www.cp2k.org/exercises:2017_ethz_mmm:nacl_free_energy?s[]=target. 
However, they don't explain what CP2K is doing when you specify a target. 

Does this method, for example, allow you to place two atoms 10A away and 
set TARGET to 1.72A? Will MD then forcibly through some sort of steepest 
descent push these two atoms towards 1.72A? Is it this simple? 

Thank you again!

Best Regards,
Devyesh Rana

On Monday, November 2, 2020 at 3:23:24 AM UTC-5, Marcella Iannuzzi wrote:
> Dear Devyesh Rana
> You can run a series of MD with restraints, i.e., following an Umbrella 
> Sampling procedure.
> You can run a series of MD with constraints, sampling the corresponding 
> Lagrangian multiplier, i.e., following a Thermodynamic Integration 
> procedure. 
> You can run MD with constraints, specifying  a target, a target_growth, 
> and a target_limit to steer the change along the MD.
> Kind regards
> Marcella
> On Friday, October 30, 2020 at 9:06:04 PM UTC+1 Dev Rana wrote:
>> Is there an easy way of preconfiguring a system for steered molecular 
>> dynamics?
>> Specifically, I'd like to understand a reaction in a solvent via AIMD. 
>> However, instead of waiting for spontaneous reactions to occur, I'd like to 
>> forcibly make particles interact. Using the potential of mean force to 
>> obtain transition states etc. Is there an easy way to constrain atoms and 
>> automatically have them incrementally move towards each other?
>> I think the nudged elastic band method might help, but this may not be 
>> the best avenue. 
>> Any suggestions?
>> Best Regards,
>> Devyesh Rana
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