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<div class="moz-cite-prefix">Hi Berk,<br>
<br>
thank you, excellent!<br>
When will this be available?<br>
<br>
Cheers<br>
Sabine<br>
<br>
<br>
Am 13.02.2015 14:58, schrieb Berk Hess:<br>
</div>
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<div class="moz-cite-prefix">Hi,<br>
<br>
Does <a moz-do-not-send="true" class="moz-txt-link-freetext"
href="https://gerrit.gromacs.org/#/c/3947/">https://gerrit.gromacs.org/#/c/3947/</a>
do what you want?<br>
<br>
Cheers,<br>
<br>
Berk<br>
<br>
On 2015-02-13 14:41, Sabine Reisser wrote:<br>
</div>
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Hi again,<br>
<br>
I think this topic is still interesting.<br>
I have just tested Jochens code for flat-bottom position
restraints, which works great, but unfortunately it's not
suitable for what I need.<br>
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.<br>
<br>
So I'd be grateful if you could reconsider including the
extension to the pull code described below.<br>
<br>
Cheers<br>
Sabine<br>
<br>
<br>
<br>
<br>
<br>
--------------------------------------------------------------------------------------<br>
<pre>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:
><i> It's been in master branch for about a year :-)
</i>><i>
</i>><i> Mark
</i>><i>
</i>><i>
</i>><i> On Wed, Feb 12, 2014 at 8:20 PM, Berk Hess <<a moz-do-not-send="true" href="https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-developers">hess at kth.se</a>
</i>><i> <mailto:<a moz-do-not-send="true" href="https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-developers">hess at kth.se</a>>> wrote:
</i>><i>
</i>><i> On 02/12/2014 04:55 PM, David van der Spoel wrote:
</i>><i>
</i>><i> On 2014-02-12 15:24, Sabine Reisser wrote:
</i>><i>
</i>><i> Hi,
</i>><i>
</i>><i> "It seems like your potential would not need an extra
</i>><i> parameter (it
</i>><i> should
</i>><i> equal a flat bottomed potential with lower limit 0)."
</i>><i>
</i>><i> A flat bottom potential is already in the code and we have
</i>><i> used it extensively. Jochen Hub has implemented it.
</i>><i>
</i>><i> Not in the main distribution.
</i>><i>
</i>><i> Cheers,
</i>><i>
</i>><i> Berk
</i>><i>
</i>><i>
</i>><i> Yes, this is exactly what I mean.
</i>><i>
</i>><i> Thanks & cheers
</i>><i> Sabine
</i>><i>
</i>><i>
</i>><i>
</i>><i> On 02/12/2014 03:08 PM, Berk Hess wrote:
</i>><i>
</i>><i> Hi,
</i>><i>
</i>><i> This indeed looks like a flat-bottomed restraint
</i>><i> potential. I had
</i>><i> proposed that addition to the pull code for 5.0 in a
</i>><i> request for
</i>><i> feedback, which I also posted to the developers list.
</i>><i> But since I didn't
</i>><i> receive any response on this point I didn't implement
</i>><i> it. Also because a
</i>><i> general flat bottomed potential needs an extra
</i>><i> (distance) parameter. It
</i>><i> seems like your potential would not need an extra
</i>><i> parameter (it should
</i>><i> equal a flat bottomed potential with lower limit 0).
</i>><i> Since it's too late
</i>><i> for 5.0, I would propose to implement the flat
</i>><i> bottomed potential for
</i>><i> 5.1.
</i>><i>
</i>><i> Cheers,
</i>><i>
</i>><i> Berk
</i>><i>
</i>><i> On 02/12/2014 02:31 PM, Shirts, Michael (mrs5pt) wrote:
</i>><i>
</i>><i> Hi, Sabine-
</i>><i>
</i>><i> So, this looks like the distance restraint
</i>><i> potential (bond function
</i>><i> 10) in
</i>><i> section 4.3.4 of the manual that matches this
</i>><i> potential function. Right
</i>><i> now, this potential can only be applied. However,
</i>><i> there is a planned
</i>><i> fix
</i>><i> for 5.0 that will include the ability to add all
</i>><i> bonded interactions in
</i>><i> between arbitrary atoms in the system, even if
</i>><i> they are not in the same
</i>><i> molecule.
</i>><i>
</i>><i> I BELIEVE there is an extension to the pull code
</i>><i> that would allow
</i>><i> general
</i>><i> bonded potentials to be used between COMs of index
</i>><i> groups as well but
</i>><i> I'm
</i>><i> not as certain about that.
</i>><i>
</i>><i> I think that these planned changes will capture
</i>><i> the functionality
</i>><i> that you
</i>><i> are describing. Is that correct?
</i>><i>
</i>><i> Best,
</i>><i>
</i>><i> ~~~~~~~~~~~~
</i>><i> Michael Shirts
</i>><i> Assistant Professor
</i>><i> Department of Chemical Engineering
</i>><i> University of Virginia
</i>><i> <a moz-do-not-send="true" href="https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-developers">michael.shirts at virginia.edu</a>
</i>><i> <mailto:<a moz-do-not-send="true" href="https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-developers">michael.shirts at virginia.edu</a>>
</i>><i> (434)-243-1821
</i>><i>
</i>><i>
</i>><i>
</i>><i> On 2/12/14, 8:20 AM, "Sabine Reisser"
</i>><i> <<a moz-do-not-send="true" href="https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-developers">sabine.reisser at kit.edu</a>
</i>><i> <mailto:<a moz-do-not-send="true" href="https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-developers">sabine.reisser at kit.edu</a>>> wrote:
</i>><i>
</i>><i> Hello,
</i>><i>
</i>><i> I have implemented an extension to the
</i>><i> existing umbrella code in
</i>><i> Gromacs
</i>><i> version 4.6.3. It is a semiharmonic potential
</i>><i> which sets a maximum
</i>><i> distance between two index groups. When this
</i>><i> distance is trespassed, a
</i>><i> force kicks in and bounces the pull group
</i>><i> back, when the distance is
</i>><i> below the threshold, motions are completely
</i>><i> unrestrained. I use this
</i>><i> code to simulate pores of antimicrobial
</i>><i> peptides, to keep the peptides
</i>><i> in close vicinity without actually interfering
</i>><i> with the pore formation
</i>><i> process.
</i>><i> The code can also be used to make sure several
</i>><i> peptides bind to the
</i>><i> same
</i>><i> side of a membrane or in ligand-binding
</i>><i> simulations.
</i>><i> The relevant part of the extended code is no
</i>><i> longer than 10 lines,
</i>><i> but I
</i>><i> naturally had to change other files in order
</i>><i> to read the modified input
</i>><i>
</i>><i> >from the mdp files, too. Affected binaries are
</i>><i> mdrun and grompp.
</i>><i>
</i>><i> Instead of providing this singular modified
</i>><i> Gromacs 4.6.3 as a tarball
</i>><i> for downloading, I would like to get this
</i>><i> extension into the official
</i>><i> release so that it is maintained also in
</i>><i> future releases.
</i>><i>
</i>><i> What is the procedure to achieve this or who
</i>><i> is the best person to
</i>><i> address?
</i>><i>
</i>><i> With best regards
</i>><i>
</i>><i> Sabine Reißer
</i>><i>
</i>><i>
</i>><i> ---------------------------------
</i>><i> Dipl. phys. Sabine Reißer
</i>><i> Theoretical Chemical Biology
</i>><i> Institute for Physical Chemistry
</i>><i> Karlsruhe Institute for Technology (KIT)
</i>><i> Germany
</i>><i>
</i>><i>
</i>><i>
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<pre class="moz-signature" cols="72">--
Dipl. Phys. Sabine Reißer
Karlsruhe Institute of Technology (KIT)
Institute of Physical Chemistry
Phone +49 (0) 721 / 608-45070</pre>
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<pre class="moz-signature" cols="72">--
Dipl. Phys. Sabine Reißer
Karlsruhe Institute of Technology (KIT)
Institute of Physical Chemistry
Phone +49 (0) 721 / 608-45070</pre>
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