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
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--
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 - 07:00:04 PST
