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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Received on Mon Feb 08 2016 - 07:00:03 PST
