[gmx-users] Free energy between residues

[lloyd riggs]

>>> I work in UK, London. Why are you asking?

Because Im a super cop.  No I just woundered about people with gmail, yahoo, or like mine gmx as to where they are at, etc...

Ive been doing something similar, and it fits with whats expected, however what Justin said is true, without knowing what your doing, or how inclusivly your doing it, it may or may not make sense.  In my case I may either be lucky, or something of the sort...

That, and I was trying to post a little, as I read the post extensivly and find them helpfull sometimes...but post little other than a lame thing here and there.  

Stephan Watkins
University of Bern,
Department of Allergy, rheumatology and immunology
Bern 3011
Switzerland
0041 31 632 43 22/42 33

-------- Original-Nachricht --------
> Datum: Thu, 28 Jun 2012 07:19:14 -0400
> Von: "Justin A. Lemkul" <jalemkul at vt.edu>
> An: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Betreff: Re: [gmx-users] Free energy between residues

> 
> 
> On 6/28/12 6:51 AM, Steven Neumann wrote:
> > On Thu, Jun 28, 2012 at 11:42 AM, Justin A. Lemkul <jalemkul at vt.edu>
> wrote:
> >>
> >>
> >> On 6/28/12 6:33 AM, Steven Neumann wrote:
> >>>
> >>> On Thu, Jun 28, 2012 at 11:20 AM, lloyd riggs <lloyd.riggs at gmx.ch>
> wrote:
> >>>>
> >>>> Dear Steven,
> >>>>
> >>>> Where are you working?
> >>>
> >>>
> >>> I work in UK, London. Why are you asking?
> >>>
> >>>
> >>>> >From my experience the g_energy  -fee only gives a free enrgy
> estimate
> >>>> for the whole system, so one has to pull out all the energy terms
> based on
> >>>> your index file of interest and sum them in a spread sheet.  if the
> -fee can
> >>>> do the energy estimates for a specific set, please let me know this
> would be
> >>>> valuable to me.
> >>>
> >>>
> >>> I think I will just need a potential energy between those residues (LR
> >>> and Coulombic) and then can get the effective potential
> >>> Ueff=-kTln<e(-BU)
> >>> and then g_dist.
> >>>
> >>
> >> If you are using PME, there is no trivial way to decompose the
> reciprocal
> >> space term.
> >>
> >> -Justin
> >
> > But if I will get the effective potential with respect to the distance
> > I can adjust non bonded parameters to this curve in coarse grained
> > model. Am I right?
> >
> 
> Honestly, I have no idea on what intend to adjust.  Certainly you can
> tweak 
> things in any way you like, but that doesn't mean the answer makes sense
> or that 
> what you've done is justifiable.  To me, umbrella sampling seems far more 
> straightforward.
> 
> -Justin
> 
> -- 
> ========================================
> 
> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> 
> ========================================
> 
> 
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