[gmx-developers] Umbrella code extension / flat bottom potential
Berk Hess
hess at kth.se
Fri Feb 13 15:22:36 CET 2015
It will be in 5.1, for which a beta should be out soon.
But you can pull the change from the link I sent if you want to use it now.
Berk
On 2015-02-13 15:17, Sabine Reisser wrote:
> Hi Berk,
>
> thank you, excellent!
> When will this be available?
>
> Cheers
> Sabine
>
>
> Am 13.02.2015 14:58, schrieb Berk Hess:
>> Hi,
>>
>> Does https://gerrit.gromacs.org/#/c/3947/ do what you want?
>>
>> Cheers,
>>
>> Berk
>>
>> On 2015-02-13 14:41, Sabine Reisser wrote:
>>> 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
>>>
>>>
>>
>
>
> --
> Dipl. Phys. Sabine Reißer
> Karlsruhe Institute of Technology (KIT)
> Institute of Physical Chemistry
>
> Phone +49 (0) 721 / 608-45070
>
>
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