[gmx-developers] Umbrella code extension / flat bottom potential
Berk Hess
hess at kth.se
Thu Feb 13 08:50:53 CET 2014
I guess you mean flat-bottomed position restraints.
I am talking about the pull code (between COM iso atoms).
Berk
On 02/13/2014 04:05 AM, Mark Abraham wrote:
> It's been in master branch for about a year :-)
>
> Mark
>
>
> On Wed, Feb 12, 2014 at 8:20 PM, Berk Hess <hess at kth.se
> <mailto:hess at kth.se>> wrote:
>
> On 02/12/2014 04:55 PM, David van der Spoel wrote:
>
> On 2014-02-12 15:24, Sabine Reisser wrote:
>
> Hi,
>
> "It seems like your potential would not need an extra
> parameter (it
> should
> equal a flat bottomed potential with lower limit 0)."
>
> A flat bottom potential is already in the code and we have
> used it extensively. Jochen Hub has implemented it.
>
> Not in the main distribution.
>
> Cheers,
>
> Berk
>
>
> Yes, this is exactly what I mean.
>
> Thanks & cheers
> Sabine
>
>
>
> On 02/12/2014 03:08 PM, Berk Hess wrote:
>
> Hi,
>
> This indeed looks like a flat-bottomed restraint
> potential. I had
> proposed that addition to the pull code for 5.0 in a
> request for
> feedback, which I also posted to the developers list.
> But since I didn't
> receive any response on this point I didn't implement
> it. Also because a
> general flat bottomed potential needs an extra
> (distance) parameter. It
> seems like your potential would not need an extra
> parameter (it should
> equal a flat bottomed potential with lower limit 0).
> Since it's too late
> for 5.0, I would propose to implement the flat
> bottomed potential for
> 5.1.
>
> Cheers,
>
> Berk
>
> On 02/12/2014 02:31 PM, Shirts, Michael (mrs5pt) wrote:
>
> Hi, Sabine-
>
> So, this looks like the distance restraint
> potential (bond function
> 10) in
> section 4.3.4 of the manual that matches this
> potential function. Right
> now, this potential can only be applied. However,
> there is a planned
> fix
> for 5.0 that will include the ability to add all
> bonded interactions in
> between arbitrary atoms in the system, even if
> they are not in the same
> molecule.
>
> I BELIEVE there is an extension to the pull code
> that would allow
> general
> bonded potentials to be used between COMs of index
> groups as well but
> I'm
> not as certain about that.
>
> I think that these planned changes will capture
> the functionality
> that you
> are describing. Is that correct?
>
> Best,
>
> ~~~~~~~~~~~~
> Michael Shirts
> Assistant Professor
> Department of Chemical Engineering
> University of Virginia
> michael.shirts at virginia.edu
> <mailto:michael.shirts at virginia.edu>
> (434)-243-1821
>
>
>
> On 2/12/14, 8:20 AM, "Sabine Reisser"
> <sabine.reisser at kit.edu
> <mailto:sabine.reisser at kit.edu>> wrote:
>
> Hello,
>
> I have implemented an extension to the
> existing umbrella code in
> Gromacs
> version 4.6.3. It is a semiharmonic potential
> which sets a maximum
> distance between two index groups. When this
> distance is trespassed, a
> force kicks in and bounces the pull group
> back, when the distance is
> below the threshold, motions are completely
> unrestrained. I use this
> code to simulate pores of antimicrobial
> peptides, to keep the peptides
> in close vicinity without actually interfering
> with the pore formation
> process.
> The code can also be used to make sure several
> peptides bind to the
> same
> side of a membrane or in ligand-binding
> simulations.
> The relevant part of the extended code is no
> longer than 10 lines,
> but I
> naturally had to change other files in order
> to read the modified input
>
> >from the mdp files, too. Affected binaries are
> mdrun and grompp.
>
> Instead of providing this singular modified
> Gromacs 4.6.3 as a tarball
> for downloading, I would like to get this
> extension into the official
> release so that it is maintained also in
> future releases.
>
> What is the procedure to achieve this or who
> is the best person to
> address?
>
> With best regards
>
> Sabine Reißer
>
>
> ---------------------------------
> Dipl. phys. Sabine Reißer
> Theoretical Chemical Biology
> Institute for Physical Chemistry
> Karlsruhe Institute for Technology (KIT)
> Germany
>
>
>
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