[gmx-developers] Umbrella code extension / flat bottom potential
Sabine Reisser
sabine.reisser at kit.edu
Tue Feb 17 11:24:02 CET 2015
Hi Jochen,
thanks! In the meantime my PhD student found the -r option, too.
I can also just use editconf to create a shifted reference structure, right?
Cheers
Sabine
Am 17.02.2015 09:36, schrieb Jochen Hub:
> 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/
> ---------------------------------------------------
--
Dipl. Phys. Sabine Reißer
Karlsruhe Institute of Technology (KIT)
Institute of Physical Chemistry
Phone +49 (0) 721 / 608-45070
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