[gmx-developers] Umbrella code extension / flat bottom potential
Sabine Reisser
sabine.reisser at kit.edu
Tue Feb 17 13:55:45 CET 2015
One more question (I know this conservation starts to belong on the
users list):
Is there a way to define two variables in "define" in the mdp file? I
would like distance restraints AND fb position restraints (DISRES and
POSRES).
Cheers
Sabine
Am 17.02.2015 13:25, schrieb Sabine Reisser:
> 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
>>>>> />/
>>>>> />/
>>>>> />/
>>>>> />/ --
>>>>> />/ Gromacs Developers mailing list
>>>>> />/
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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
>
> --
> Gromacs Developers mailing list
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--
Dipl. Phys. Sabine Reißer
Karlsruhe Institute of Technology (KIT)
Institute of Physical Chemistry
Phone +49 (0) 721 / 608-45070
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