[gmx-developers] Umbrella code extension / flat bottom potential
Justin Lemkul
jalemkul at vt.edu
Tue Feb 17 13:57:57 CET 2015
On 2/17/15 7:55 AM, Sabine Reisser wrote:
> 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).
>
define = -DPOSRES -DDISRES -DWhateverElseYouWant
-Justin
> 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
>>>>>> />/
>>>>>> />/ * Please search the archive at
>>>>>> />/
>>>>>> http://www.gromacs.org/Support/Mailing_Lists/GMX-developers_List
>>>>>> />/ before
>>>>>> />/ posting!
>>>>>> />/
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>>>>>> />/
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>>>>>>
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>>>>>> gromacs.org
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>>>>>>
>>>>>> />/
>>>>>> />/
>>>>>> />/
>>>>>> />/
>>>>>> />/
>>>>>> />/ --
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>>>>>> />/
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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
>>
>> --
>> Gromacs Developers mailing list
>>
>> * Please search the archive at
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>
>
--
==================================================
Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalemkul at outerbanks.umaryland.edu | (410) 706-7441
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