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_coms...@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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