[gmx-developers] Umbrella code extension / flat bottom potential
Sabine Reisser
sabine.reisser at kit.edu
Tue Feb 17 13:25:32 CET 2015
Ok, it works! Thanks!
Cheers
Sabine
Am 17.02.2015 12:41, schrieb Jochen Hub:
>
> Am 17/02/15 um 11:23 schrieb Sabine Reisser:
>> 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?
> That depends on what exactly you want. With editconf -translate, the
> atoms in your peptide will have different Z coordinates.
>
> Let's say you want all atoms in your pepetide to feel the same FB-posres
> potential, with the same center of the potential (e.g. the center of the
> membrane), then you would need to use the same Z-cooridinate in the
> posres-reference.pdb file (the one passed with -r) for all atoms in your
> peptide.
>
> Best,
> Jochen
>
>
>> 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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>>>> />/
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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/
>>> ---------------------------------------------------
>>
> --
> ---------------------------------------------------
> 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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