Dear Gromacs users
I had posted a similar question recently, but I did not get any reply so I
think I did not put it correctly.
It is regarding thermodynamic integration of mutating (not decoupling ) VDW
parameters from state A to state B. Will different state B parameters have
different values
Hi Alex,
I thought by getting the flat-bottom restraint potential on my target molecule
I should be able to get the free energy of unbiased case.
Basically; P(q)=P’(q)exp(V(q)/kBT) Here P is unbiased probability, P’ is biased
probability and V is added potential.
However I am not totally sure.
Hi Gozde,
I also use something similar, by an simple pull restrain(distance) to keep
a counter ion close to the charged molecule which is under perturbation in
FEP.
These type of restrains are \*Lambda *independent and if I am not wrong
their portion in free energy change should be calculated ana
Any idea?
Thanks.
> On 13 Oct 2016, at 15:42, gozde ergin wrote:
>
> Dear all,
>
> I will use Gromacs to calculate the chemical potential difference of
> solvation a surfactant molecule on the surface.
> System covers water molecules covered with surfactant molecules.
> I will apply flat-bottom
Dear all,
I will use Gromacs to calculate the chemical potential difference of solvation
a surfactant molecule on the surface.
System covers water molecules covered with surfactant molecules.
I will apply flat-bottom restraint to the surfactant molecules in order to
stabilise them on surface. I
Dear all,
I will use Gromacs to calculate the chemical potential difference of solvation
a surfactant molecule on the surface.
System covers water molecules covered with surfactant molecules.
I will apply flat-bottom restraint to the surfactant molecules in order to
stabilise them on surface. I
TI/FEP are appropriate when you have "small" changes between states.
Whether you delete/create all of a molecule or just part of it doesn't
matter that much. So a relative simulation between a glycated and
non-glycated sounds quite reasonable to me. Of course, this will become
increasingly more d
Hi Mark,
I will give that a thorough read. I was wondering if you could possibly
comment on whether TI is an appropriate tool for calculating the free
energy difference between two states, A―> non-glycated side chain, and b―>
glycated side chain? Most examples given focus on the inclusion/exclusio
Hi,
Also you might consider pmx
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4365728/ for such topology
generation. There is further work in the pipeline, so do get in touch with
Bert if there's something of interest.
Mark
On Mon, Apr 18, 2016 at 11:56 AM Nash, Anthony wrote:
> From the site, “
From the site, “..or the free energy of a mutation of a side chain.”
I think this is what I am after. Many thanks for the link.
Anthony
On 18/04/2016 10:42, "gromacs.org_gmx-users-boun...@maillist.sys.kth.se on
behalf of Hannes Loeffler"
wrote:
>A good starting point is http://www.alchemistr
A good starting point is http://www.alchemistry.org/ which has quite a
lot of detail on relative alchemical free energy simulations (not only
TI).
On Mon, 18 Apr 2016 09:27:02 +
"Nash, Anthony" wrote:
> Hi all,
>
> I¹m looking for a guide on performing TI between a protein in its
> crystal
Hi all,
I¹m looking for a guide on performing TI between a protein in its crystal
periodicity with a particular residue (state A), to the same system but
with a different residue (state B).
I¹m currently using
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/free
_energy/01_
how can we use Thermodynamic integration in gromacs for free energy
analysis.any tutorial/script pleaseRegards Sana Saeed
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