Re: [gmx-users] Hydrophobic interaction analysis

[David van der Spoel]

On 11/11/16 03:53, Mijiddorj Batsaikhan wrote:

Dear gmx users,

I simulated several peptide's folding. I would like to know the effects of
hydrophobic interaction for the folding. How can I make analysis and know
the effect of hydrophobic interaction?
Is it possible to assess the hydrophobic interaction using short range Van
der  Waals force?

Hydrophobic interactions do not exist. There is however, a hydrophobic 
effect, see, e.g.


http://pubs.acs.org/doi/abs/10.1021/jp015514e
http://www.nature.com/nature/journal/v437/n7059/abs/nature04162.html

What you can attempt is to compute enthalpy and entropy (but only if you 
have explicit water):

http://journals.aps.org/prl/abstract/10.1103/PhysRevLett.96.238102


Best regards,

Mijiddorj




--
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Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205.
sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se
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[gmx-users] Hydrophobic interaction analysis

[Mijiddorj Batsaikhan]

Dear gmx users,

I simulated several peptide's folding. I would like to know the effects of
hydrophobic interaction for the folding. How can I make analysis and know
the effect of hydrophobic interaction?
Is it possible to assess the hydrophobic interaction using short range Van
der  Waals force?


Best regards,

Mijiddorj
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Re: [gmx-users] Hydrophobic interaction analysis

[Justin Lemkul]

On 5/13/16 8:23 AM, Nikhil Maroli wrote:

We can analyse hydrogen bond numbers, what about total hydrogen bond
energy between two molecules over time like that in case of hydrophobic


There is no such energy term.  A hydrogen bond is largely electrostatic, though, 
so short-range Coulombic energies might tell you something.  But if you try to 
claim some energy of a specific interaction, it would be unphysical.


-Justin


interaction,is there any possibility to know the energy involved in the
process



--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
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Re: [gmx-users] Hydrophobic interaction analysis

[Nikhil Maroli]

We can analyse hydrogen bond numbers, what about total hydrogen bond 
energy between two molecules over time like that in case of hydrophobic 
interaction,is there any possibility to know the energy involved in the 
process  

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Re: [gmx-users] Hydrophobic interaction analysis

[Sun Iba]

hi
Its hydrophobic effect, Nikhil. And you can make index of hydrophobic
groups in your protein, then calculate distance between them.

On Thu, May 12, 2016 at 11:03 PM, Nikhil Maroli  wrote:

> Dear all,
>
> is there any option in gromacs to study the hydrophobic interaction between
> the two molecule over the simulation time !
> --
> Ragards,
> Nikhil Maroli
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[gmx-users] Hydrophobic interaction analysis

[Nikhil Maroli]

Dear all,

is there any option in gromacs to study the hydrophobic interaction between
the two molecule over the simulation time !
-- 
Ragards,
Nikhil Maroli
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