[gmx-developers] Umbrella code extension / flat bottom potential
Jochen Hub
jhub at gwdg.de
Tue Feb 17 12:41:41 CET 2015
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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>>>
>>> --
>>> 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/
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