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 Sun Feb 07 2016 - 13:00:02 PST
