[gmx-developers] Umbrella code extension / flat bottom potential
Sabine Reisser
sabine.reisser at kit.edu
Tue Feb 17 14:02:52 CET 2015
Thanks! Might be something worth to include in the manual.
Cheers
Sabine
Am 17.02.2015 13:57, schrieb Justin Lemkul:
>
> 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
>>>>>>> />/
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>>>>>>> />/ posting!
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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
>>>
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>>> send a mail to gmx-developers-request at gromacs.org.
>>
> --
> ==================================================
>
> 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
> http://mackerell.umaryland.edu/~jalemkul
>
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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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