[gmx-users] Free energy calculation of Histone

[Justin Lemkul]

On 1/10/19 2:17 AM, Mark Abraham wrote:
> Hi,
>
> That's the wrong way around. :-) One doesn't do a lab experiment first and
> then decide what you wanted to observe from it, to either :-). There are
> tutorials for computing free energy of solvation, which I suggest you
> follow, and I suspect your fully solvated simulation won't be useful for
> that.

Note, however, that the alchemical approach that most tutorials use 
would never converge for something as large as a histone, let alone even 
a moderately sized polypeptide. MM/PBSA post-processing might be useful, 
but the values will be astronomical, as would (likely) the error bars.

-Justin

> Mark
>
> On Thu., 10 Jan. 2019, 02:45 Ayesha Kanwal, <ayesha_comsian at hotmail.com>
> wrote:
>
>> Dear all users,
>> I am new for using GROMACS. and also read the tutorial of Methane and
>> water. I have already simulated data of 100 ns for four histones. I want to
>> know how to calculate free energy solvation from this data. which topology
>> file and coordinate files I will use?
>> I will appreciate your good suggestions.
>>
>> Regards
>> Ayesha
>>
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-- 
==================================================

Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
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Virginia Tech Department of Biochemistry
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jalemkul at vt.edu | (540) 231-3129
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