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<div class="moz-cite-prefix">Hello,<br>
<br>
thanks as well from me for your contribution!<br>
<br>
Concerning what Erik said, I would suggest that you open an issue
on our GitLab (gitlab.com/gromacs/gromacs) so we can have the
proper discussion there.<br>
<br>
We are also having major ongoing effort for improving the free
energy code.</div>
<div class="moz-cite-prefix">So it would be great if you could join
the next developer call on the 24th so that we can discuss things
there with the rest of the developer community.<br>
<br>
Please don't hesitate to contact me for further discussions in any
case.<br>
<br>
Cheers<br>
<br>
Paul<br>
</div>
<div class="moz-cite-prefix"><br>
</div>
<div class="moz-cite-prefix">On 15/03/2021 12:34, Erik Lindahl
wrote:<br>
</div>
<blockquote type="cite"
cite="mid:1E10A755-006A-41CB-B8BB-C497A6F6EFAC@gmail.com">
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Hi Yuzhi (&Junhan)!
<div><br>
</div>
<div>First, thanks for getting involved! We love to have more
people involved, and will do our best to welcome you to the
extended team. free energy is definitely an area we want to
improve further, and contributions like the ones below sound
great.</div>
<div><br>
</div>
<div>Why don't you joint our next open developer call every second
Wednesday? Or, if the timezone makes things inconvenient we
could schedule a separate meeting.</div>
<div><br>
</div>
<div>Some of the things we will like discuss would be:</div>
<div><br>
</div>
<div>1. We are gradually moving to support both CUDA, SYCL and Hip
so we run well on all accelerators - but this also means we need
to avoid hacking things just for CUDA, and rather have a clean
hierarchical implementation where different platforms might
initially support different accelerated features. Much of this
stuff has already started to happen in gmx 2021.</div>
<div><br>
</div>
<div>2. For new features and functional forms we tend to be
restrictive, partly because it means a collective undertaking
for the entire team the next 5-10 years to ensure that feature
works with all other features. We have not quite settled things
on free energy yet, and we might consider modifying the
interactions, but we don't want 4-5 different implementations
from different teams - instead we should try to settle on which
one will serve us all best.</div>
<div><br>
</div>
<div>3. Documentation and Unit tests are critical to ensure new
code keeps working ;-)</div>
<div><br>
</div>
<div>Cheers,</div>
<div><br>
</div>
<div>Erik</div>
<div><br>
<div dir="ltr">--
<div>Erik Lindahl <a class="moz-txt-link-rfc2396E" href="mailto:erik.lindahl@scilifelab.se"><erik.lindahl@scilifelab.se></a></div>
<div>Professor of Biophysics</div>
<div>Science for Life Laboratory</div>
<div>Stockholm University & KTH</div>
<div>Office (SciLifeLab): +46 8 524 81567</div>
<div>Cell (Sweden): +46 73 4618050 </div>
<div>Cell (US): 1 267 307 8746</div>
<div><br>
</div>
</div>
<div dir="ltr"><br>
<blockquote type="cite">On Mar 15, 2021, at 12:13, Yuzhi Zhang
<a class="moz-txt-link-rfc2396E" href="mailto:352@pku.edu.cn"><352@pku.edu.cn></a> wrote:<br>
<br>
</blockquote>
</div>
<blockquote type="cite">
<div dir="ltr">
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style="margin:0px;padding:0px;border:0px;outline:0px;line-height:1.7;font-family:Tahoma,
Arial, STHeiti, SimSun;font-size:14px;">
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Dear Gromacs developers,
<div
style="margin:0px;padding:0px;border:0px;outline:0px;clear:both;">
Based on Gromacs-2020.2, we've done a series of development related to FEP in following aspects . We would like to contribute our codes to Gromacs and we're looking forward to hearing
your opinions first. </div>
<div
style="margin:0px;padding:0px;border:0px;outline:0px;clear:both;">
High-performance implementations: </div>
<div
style="margin:0px;padding:0px;border:0px;outline:0px;clear:both;">
1. Offload FEP-PME to GPU. Our status: finished.
We've also noticed that this function has been implemented in commit f7be07e3cc901eb03700d93248fc09b573370282 by M. Lundborg et. al. and has been merged in Gromacs-2021. So we won't commit this.
</div>
<div
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2. Offload non-bonded free energy
kernel to GPU. Our status: finished. </div>
<div
style="margin:0px;padding:0px;border:0px;outline:0px;clear:both;">
3. Offload bonded free energy
kernel to GPU. Our status: finished. </div>
<div
style="margin:0px;padding:0px;border:0px;outline:0px;clear:both;">
4. Support GPU updates for
FEP. Our status: finished md-integrator.
We've noticed that this has also been implemented in Gromacs-2021, but we'are still interested in supporting GPU updates of sd-integrator. Similar discussion can be found in issue #3258 on gitlab.
</div>
<div
style="margin:0px;padding:0px;border:0px;outline:0px;clear:both;">
5. Support GPU replica exchange. Our status:
finished. </div>
<div
style="margin:0px;padding:0px;border:0px;outline:0px;clear:both;">
<br>
</div>
<div
style="margin:0px;padding:0px;border:0px;outline:0px;clear:both;">
New features: </div>
<div
style="margin:0px;padding:0px;border:0px;outline:0px;clear:both;">
1. Support "Soft Bond Potential" in FEP, which is proposed in DOI: 10.1021/acs.jctc.6b00991 and allows a more smooth change of bond topology when there is bond formation or breaking in a FEP transformation, such as 5-member ring to 6-member ring. Our status: finished.
</div>
<div
style="margin:0px;padding:0px;border:0px;outline:0px;clear:both;">
2. Split softcore parameters for VDW and Coulomb interactions. We noticed that currently Gromacs supports only one parameter "sc-alpha" to modify soft-core interactions. After our tests, this will cause a phase-transition-like phenomenon at middle lambdas in some cases. Our status: finished. We also noticed recently there
have been some new forms of softcores like gapsys softcore (DOI: dx.doi.org/10.1021/ct300220p and discussed in <a
href="https://gitlab.com/gromacs/gromacs/-/merge_requests/882"
target="_blank" moz-do-not-send="true">https://gitlab.com/gromacs/gromacs/-/merge_requests/882</a> ) and Amber SSC2 softcore (DOI: 10.1021/acs.jctc.0c00237.) And we would like to ask if you consider it's necessary to support such new softcore potentials.
</div>
<div
style="margin:0px;padding:0px;border:0px;outline:0px;clear:both;">
These terms are all that we want to contribute to Gromacs. But we have to admit that there is still a lot of work to test and standardize our codes to meet all requirements of Gromacs. Is there any suggestion?
</div>
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<br>
</div>
<div
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Best wishes! </div>
<div
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Happy Simulating!<br>
</div>
<div
style="margin:0px;padding:0px;border:0px;outline:0px;clear:both;">
Yuzhi & Junhan </div>
</div>
</div>
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<br style="font-family:Helvetica, Tahoma,
Arial;font-size:14px;white-space:normal;">
</div>
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</blockquote>
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<br>
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<p><br>
</p>
<pre class="moz-signature" cols="72">--
Paul Bauer, PhD
GROMACS Development Manager
KTH Stockholm, SciLifeLab
0046737308594</pre>
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