Thanks Callum and Adrian,
However, I haven't that time I'll try to do ASMD (generally following
tutorial) between ligand and atom(s) of the middle plane of bilayer (this
time decreasing distance). I just do not know is this correct but it is
worth of try. Since I just wish to establish relative order of ligands
permeability through the bilayer (I don't have experimental data) the exact
free energy wouldn't be of prevalent significance. I think that
PMF-timescale evaluated by this method can serve for this purpose.
Have a nice day all of u
Zoran
-----Original Message-----
From: Adrian Roitberg
Sent: Monday, February 8, 2016 3:38 PM
To: AMBER Mailing List ; Jason Swails ; zoran matovic
Subject: Re: [AMBER] Z-constraint PMF method
spoiler alert:
there is a chance it will be available in amber16...
I have seen beta versions around.
adrian
On 2/8/16 9:36 AM, Dickson, Callum J wrote:
> Hi Zoran,
>
> The z-constraint PMF method is not available in AMBER and I don't believe
> there are plans to insert it into the code anytime soon. However the
> center-of-mass umbrella restraint method will be available in the upcoming
> AMBER 16 release (in pmemd CPU and GPU) - this is what Jason is referring
> to. This method, combined with WHAM, allows the calculation of free energy
> of transfer profiles to move across a membrane bilayer and a diffusion
> estimate, essentially identical information to using the z-constraint.
>
> I do not have experience with ASMD so cannot comment on whether it is
> suitable for such calculations.
> All the best,
> Callum
>
> ________________________________________
> From: zoran matovic <zmatovic.kg.ac.rs>
> Sent: Sunday, February 7, 2016 4:07 PM
> To: Jason Swails; AMBER Mailing List
> Subject: Re: [AMBER] Z-constraint PMF method
>
> Thanks Jason,
> My excuses to all for my impatience.
> I’m at the end of computations and just want to do all the calcs with
> Amber even it would be less accurate. In the meantime I’ll wait for what
> others say.
>
> Cheers
> Zoran
>
> From: Jason Swails
> Sent: Sunday, February 7, 2016 9:50 PM
> To: zoran matovic ; AMBER Mailing List
> Subject: Re: [AMBER] Z-constraint PMF method
>
>
>
> On Sun, Feb 7, 2016 at 1:28 PM, zoran matovic <zmatovic.kg.ac.rs> wrote:
>
> Seem that there is no suggestion here. So I kindly ask again
> (especially
> Amber people) if possible to clarify this issue.
>
> You should give longer than a day for knowledgeable people to respond
> before re-asking a question, *especially* when asking on a weekend
> (realize that you haven't even provided people with a single business day
> to respond before asking a second time). I'm pretty sure this is
> impossible in the current version of the code but I think that the
> upcoming release will support this kind of restraint -- given my
> uncertainty about whether the release in April will support this, I was
> going to let someone else respond. You might be able to use point-plane
> restraints (sander only, no GPU) to do what you want, but I'm not sure
> about that.
>
> I wish to additionally ask
> why don't we can use ASMD given in amber tutorial. I repeated this and
> lipid tutorial successfully and found them feasible within reasonable
> computational cost. What's the difference between ASMD and
> "z-constraint PMF
> method"?
>
>
> Depends. ASMD is a protocol for performing steered MD using a particular
> restraint. z-restraints refer to a specific functional form of the
> restraint potentials (involving only the z-coordinate). You can do
> steered MD using z-restraints if you want, or you can do umbrella sampling
> using z-restraints.
>
> --
>
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
--
Dr. Adrian E. Roitberg
Professor.
Department of Chemistry
University of Florida
roitberg.ufl.edu
352-392-6972
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Received on Mon Feb 08 2016 - 07:30:03 PST
