[gmx-developers] Umbrella code extension / flat bottom potential
Jochen Hub
jhub at gwdg.de
Tue Feb 17 09:36:04 CET 2015
Hi Sabine,
the reference positions for the flat-bottom posres are the same as for
the normal position-restraints. And those can be specified in a pdb/gro
file given to grompp with option -r. So you need to take your initial
file, and change the z-coordinate of the restrained atom to the the
center of of FB-potential, and use grompp -r.
Tip of the day :) : to change the Z-column of a PDB file, you can use
the bash function:
pdb_replace_z ()
{
local x="$(printf '%8.3f' $1)";
sed -E "s/^(.{46})(.{8})(.*)$/\1${x}\3/"
}
Best,
Jochne
Am 13/02/15 um 14:41 schrieb Sabine Reisser:
> 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
>
> Phone +49 (0) 721 / 608-45070
>
>
>
--
---------------------------------------------------
Dr. Jochen Hub
Computational Molecular Biophysics Group
Institute for Microbiology and Genetics
Georg-August-University of Göttingen
Justus-von-Liebig-Weg 11, 37077 Göttingen, Germany.
Phone: +49-551-39-14189
http://cmb.bio.uni-goettingen.de/
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