You need to read the metadynamics papers. That is what I mean by amber.
This is NOT an amber-related question, it is a question a particular
method, and it is best answered by reading the original papers.
On 10/17/13 12:08 PM, Ravi Tripathi wrote:
> Dear Mr. Adrian,
> Yes, I posted my question to amber list only. Thanks alot for your kind
> reply.
> But the doubt still remains the same : If the Gaussian are added to the
> PES then how we have the measures of FES from the metadynamics simulation.
> The reconstructed surface should be the PES not FES.
> Thank you in advance.
>
>
> On Thu, Oct 17, 2013 at 8:31 PM, Adrian Roitberg <roitberg.ufl.edu> wrote:
>
>> They are added to the PES. You never run dynamics in the free energy
>> surface. Of course, the shape of the PES and the free energy suraces
>> tend to be similar.
>>
>> BTW: I am not sure why you ask this question to the amber list.
>>
>> Adrian
>>
>> On 10/17/13 10:59 AM, Ravi Tripathi wrote:
>>> Dear all,
>>> I have a doubt related to the metadynamics simulation.The dynamics of
>>> nuclei is on the potential energy surface. Since the idea behind
>>> meta-dynamics is to add the Gaussian to surmount the free energy
>> surface,
>>> so the doubt is whether the Gaussians are being added to the PES surface
>>> where nuclei moves or on the Free energy surface. Any answer related to
>>> this will be highly appreciated.
>>>
>> --
>> Dr. Adrian E. Roitberg
>>
>> Colonel Allan R. and Margaret G. Crow Term Professor.
>> Quantum Theory Project, Department of Chemistry
>> University of Florida
>> roitberg.ufl.edu
>> 352-392-6972
>>
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
--
Dr. Adrian E. Roitberg
Colonel Allan R. and Margaret G. Crow Term Professor.
Quantum Theory Project, Department of Chemistry
University of Florida
roitberg.ufl.edu
352-392-6972
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Received on Thu Oct 17 2013 - 09:30:03 PDT
