His title is Dr. Roitberg, not Mr.
And his point is that the primary purpose of the mailing list is to address questions in how to use Amber rather than general questions.
Dr. Robert Molt Jr., Ph.D.
r.molt.chemical.physics.gmail.com
Nigel Richards Research Group
Department of Chemistry & Chemical Biology
Indiana University-Purdue University Indianapolis
LD 326
402 N. Blackford St.
Indianapolis, IN 46202
> On Oct 17, 2013, at 12:08 PM, Ravi Tripathi <abhi.rt8687.gmail.com> 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
>>
>
>
>
> --
> Ravi Tripathi
> c/o Dr, Nisanth n Nair
> Research Scholar
> Department of chemistry
> IIT Kanpur
> contact me- 9648768062
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
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Received on Thu Oct 17 2013 - 09:30:03 PDT
