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<div class="moz-cite-prefix">I guess you mean flat-bottomed position
restraints.<br>
I am talking about the pull code (between COM iso atoms).<br>
<br>
Berk<br>
<br>
On 02/13/2014 04:05 AM, Mark Abraham wrote:<br>
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cite="mid:CAMNuMATkFvjJ4oA=E04unun1TykzOGRD0ahgYY_RW7USgsAF0A@mail.gmail.com"
type="cite">
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<div dir="ltr">It's been in master branch for about a year :-)
<div><br>
</div>
<div>Mark</div>
</div>
<div class="gmail_extra"><br>
<br>
<div class="gmail_quote">On Wed, Feb 12, 2014 at 8:20 PM, Berk
Hess <span dir="ltr"><<a moz-do-not-send="true"
href="mailto:hess@kth.se" target="_blank">hess@kth.se</a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0
.8ex;border-left:1px #ccc solid;padding-left:1ex">
<div class="">On 02/12/2014 04:55 PM, David van der Spoel
wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0
.8ex;border-left:1px #ccc solid;padding-left:1ex">
On 2014-02-12 15:24, Sabine Reisser wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0
.8ex;border-left:1px #ccc solid;padding-left:1ex">
Hi,<br>
<br>
"It seems like your potential would not need an
extra parameter (it<br>
should<br>
equal a flat bottomed potential with lower limit 0)."<br>
<br>
</blockquote>
A flat bottom potential is already in the code and we
have used it extensively. Jochen Hub has implemented it.<br>
</blockquote>
</div>
Not in the main distribution.<br>
<br>
Cheers,<br>
<br>
Berk
<div class="HOEnZb">
<div class="h5"><br>
<blockquote class="gmail_quote" style="margin:0 0 0
.8ex;border-left:1px #ccc solid;padding-left:1ex">
<br>
<blockquote class="gmail_quote" style="margin:0 0 0
.8ex;border-left:1px #ccc solid;padding-left:1ex">
Yes, this is exactly what I mean.<br>
<br>
Thanks & cheers<br>
Sabine<br>
<br>
<br>
<br>
On 02/12/2014 03:08 PM, Berk Hess wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0
.8ex;border-left:1px #ccc solid;padding-left:1ex">
Hi,<br>
<br>
This indeed looks like a flat-bottomed restraint
potential. I had<br>
proposed that addition to the pull code for 5.0 in
a request for<br>
feedback, which I also posted to the developers
list. But since I didn't<br>
receive any response on this point I didn't
implement it. Also because a<br>
general flat bottomed potential needs an extra
(distance) parameter. It<br>
seems like your potential would not need an extra
parameter (it should<br>
equal a flat bottomed potential with lower limit
0). Since it's too late<br>
for 5.0, I would propose to implement the flat
bottomed potential for<br>
5.1.<br>
<br>
Cheers,<br>
<br>
Berk<br>
<br>
On 02/12/2014 02:31 PM, Shirts, Michael (mrs5pt)
wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0
0 .8ex;border-left:1px #ccc
solid;padding-left:1ex">
Hi, Sabine-<br>
<br>
So, this looks like the distance restraint
potential (bond function<br>
10) in<br>
section 4.3.4 of the manual that matches this
potential function. Right<br>
now, this potential can only be applied.
However, there is a planned<br>
fix<br>
for 5.0 that will include the ability to add all
bonded interactions in<br>
between arbitrary atoms in the system, even if
they are not in the same<br>
molecule.<br>
<br>
I BELIEVE there is an extension to the pull code
that would allow<br>
general<br>
bonded potentials to be used between COMs of
index groups as well but<br>
I'm<br>
not as certain about that.<br>
<br>
I think that these planned changes will capture
the functionality<br>
that you<br>
are describing. Is that correct?<br>
<br>
Best,<br>
<br>
~~~~~~~~~~~~<br>
Michael Shirts<br>
Assistant Professor<br>
Department of Chemical Engineering<br>
University of Virginia<br>
<a moz-do-not-send="true"
href="mailto:michael.shirts@virginia.edu"
target="_blank">michael.shirts@virginia.edu</a><br>
(434)-243-1821<br>
<br>
<br>
<br>
On 2/12/14, 8:20 AM, "Sabine Reisser" <<a
moz-do-not-send="true"
href="mailto:sabine.reisser@kit.edu"
target="_blank">sabine.reisser@kit.edu</a>>
wrote:<br>
<br>
<blockquote class="gmail_quote" style="margin:0
0 0 .8ex;border-left:1px #ccc
solid;padding-left:1ex">
Hello,<br>
<br>
I have implemented an extension to the
existing umbrella code in<br>
Gromacs<br>
version 4.6.3. It is a semiharmonic potential
which sets a maximum<br>
distance between two index groups. When this
distance is trespassed, a<br>
force kicks in and bounces the pull group
back, when the distance is<br>
below the threshold, motions are completely
unrestrained. I use this<br>
code to simulate pores of antimicrobial
peptides, to keep the peptides<br>
in close vicinity without actually interfering
with the pore formation<br>
process.<br>
The code can also be used to make sure several
peptides bind to the<br>
same<br>
side of a membrane or in ligand-binding
simulations.<br>
The relevant part of the extended code is no
longer than 10 lines,<br>
but I<br>
naturally had to change other files in order
to read the modified input<br>
</blockquote>
>from the mdp files, too. Affected binaries
are mdrun and grompp.<br>
<blockquote class="gmail_quote" style="margin:0
0 0 .8ex;border-left:1px #ccc
solid;padding-left:1ex">
Instead of providing this singular modified
Gromacs 4.6.3 as a tarball<br>
for downloading, I would like to get this
extension into the official<br>
release so that it is maintained also in
future releases.<br>
<br>
What is the procedure to achieve this or who
is the best person to<br>
address?<br>
<br>
With best regards<br>
<br>
Sabine Reißer<br>
<br>
<br>
---------------------------------<br>
Dipl. phys. Sabine Reißer<br>
Theoretical Chemical Biology<br>
Institute for Physical Chemistry<br>
Karlsruhe Institute for Technology (KIT)<br>
Germany<br>
<br>
<br>
<br>
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