[gmx-developers] Umbrella code extension / flat bottom potential
Szilárd Páll
pall.szilard at gmail.com
Fri Feb 13 15:35:52 CET 2015
...and please, don't forget to give it a +1 verifyed (click on reply)
if it work as expected!
--
Szilárd
On Fri, Feb 13, 2015 at 3:17 PM, Sabine Reisser <sabine.reisser at kit.edu> 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
>> <mailto:hess at kth.se>> 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
>> <mailto:michael.shirts at virginia.edu>
>> (434)-243-1821
>>
>>
>>
>> On 2/12/14, 8:20 AM, "Sabine Reisser"
>> <sabine.reisser at kit.edu
>> <mailto:sabine.reisser at kit.edu>> 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
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> Phone +49 (0) 721 / 608-45070
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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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