[gmx-developers] Umbrella code extension / flat bottom potential
Sabine Reisser
sabine.reisser at kit.edu
Fri Feb 13 14:41:24 CET 2015
Hi again,
I think this topic is still interesting.
I have just tested Jochens code for flat-bottom position restraints,
which works great, but unfortunately it's not suitable for what I need.
Here, you can define a layer (with normal in z-direction) with a certain
thickness and invert the restraints. The problem is that you cannot
define a reference position for the layer, but the reference position is
always the initial geometry. That way, particles are pushed away from
the layer, but the direction is not defined. So I cannot use this to
bind my peptides to one leaflet of the membrane (cmp. my post "Flat
bottom position restraints" on gmx-users). Also I cannot use it to
restrain distances between molecules, which I also need sometimes.
So I'd be grateful if you could reconsider including the extension to
the pull code described below.
Cheers
Sabine
--------------------------------------------------------------------------------------
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 <https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-developers>
/>/ <mailto:hess at kth.se <https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-developers>>> 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 <https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-developers>
/>/ <mailto:michael.shirts at virginia.edu <https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-developers>>
/>/ (434)-243-1821
/>/
/>/
/>/
/>/ On 2/12/14, 8:20 AM, "Sabine Reisser"
/>/ <sabine.reisser at kit.edu <https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-developers>
/>/ <mailto:sabine.reisser at kit.edu <https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-developers>>> 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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Dipl. Phys. Sabine Reißer
Karlsruhe Institute of Technology (KIT)
Institute of Physical Chemistry
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