[gmx-users] Energy analysis

[Dallas Warren]

Always a good starting point ....

http://www.gromacs.org/Documentation/Tutorials
Catch ya,

Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3052
dallas.warren at monash.edu
---------------------------------
When the only tool you own is a hammer, every problem begins to resemble a nail.


On 20 November 2017 at 12:34, Amir Zeb <zebamir85 at gmail.com> wrote:
> Thanks Mark,
>
> Depends what you mean by "stability."
> Actually, I don't know the role of metal ion if it is used as co-factor by
> a particular protein. I thought to do comparative analysis by MD simulation
> which might predict the possible role of metal (in this case Zn^2+). Other
> analysis like RMSD, RMSF, Rg, SASA, and structural analysis etc. I have
> already done, but I want to get insight in their energetic terms while
> addressing the question why such changes occurred?
> According to the best of my study, there is no experimental data available
> for my target protein and that's why I want to predict its free-energy of
> folding or whatever else.
> Will you kindly suggest me some hand notes or tutorial like to do
> free-energy analysis for both the systems; means a) protein with metal ion
> and b) protein without metal ion?
>
> Amir
>
> On Sun, Nov 19, 2017 at 11:32 AM, Mark Abraham <mark.j.abraham at gmail.com>
> wrote:
>
>> Hi,
>>
>> Depends what you mean by "stability." A well designed study could seek to
>> measure or estimate the difference in the free-energy of folding, but that
>> would probably require an infeasibly large amount of sampling, and be
>> highly dependent on the quality of the parameterization of the
>> metal-protein interactions, for which you would probably need some suitable
>> experimental data.
>>
>> Mark
>>
>> On Sun, Nov 19, 2017 at 7:48 AM Amir Zeb <zebamir85 at gmail.com> wrote:
>>
>> > Hi gromacs users,
>> >
>> > I want to calculate the energy for comparative analysis of protein with
>> and
>> > without metal ion, wherein I would like to determine the influence of
>> metal
>> > on protein structural stability. I have used gromacs for simulation.
>> Please
>> > suggest me how to do this kind of analysis? Should i follow a specific
>> > tutorial?
>> >
>> > Amir
>> > --
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