CCL: Announce: Several MD / QC codes available for GPUs
- From: andras.borosy]*[givaudan.com
- Subject: CCL: Announce: Several MD / QC codes available for
GPUs
- Date: Thu, 1 Apr 2010 11:59:16 +0200
Dear Colleagues,
eHits docking software have been available at GPUs for year:
http://www.simbiosys.ca/whatsnew/news/index.html#20080424
Best wishes and Happy Easter!
Dr. András Péter Borosy
Scientific Modelling Expert
Fragrance Research
Givaudan Schweiz AG - Ueberlandstrasse 138 - CH-8600 - Dübendorf -
Switzerland
T:+41-44-824 2164 - F:+41-44-8242926 - http://www.givaudan.com
"Sumit Gupta sugupta]~[nvidia.com" <owner-chemistry#,#ccl.net>
Sent by: owner-chemistry+andras.borosy==givaudan.com#,#ccl.net
31.03.2010 21:44
Please respond to
"CCL Subscribers" <chemistry#,#ccl.net>
To
"Borosy, Andras " <andras.borosy#,#givaudan.com>
cc
Subject
CCL: Announce: Several MD / QC codes available for GPUs
Sent to CCL by: Sumit Gupta [sugupta:nvidia.com]
There is an early partial port of AutoDock:
http://sourceforge.net/projects/gpuautodock/
There is one more effort to port AutoDock from HCL Infosystems (they
are looking for customers interested in this port).
Earlier work on AutoDock has shown a healthy speedup
http://www.siliconinformatics.com/products.html
But this company is no longer marketing AutoDock.
There are also efforts to port Dock as well (again looking for
potential users).
A Japanese group (Akiyama et al) out of Tokyo Tech has ported
MegaDock protein-to-protein docking to CUDA.
http://research.microsoft.com/en-us/events/ersymposium2009/accelerated_clusters_proteomics_2.pdf
Sumit
----
Sumit Gupta
Sr. Manager - Tesla GPU HPC Group
NVIDIA
-----Original Message-----
> From: owner-chemistry+sugupta==nvidia.com\a/ccl.net
[mailto:owner-chemistry+sugupta==nvidia.com\a/ccl.net] On
Behalf Of Carlos
F. Lagos cflagos-,-uc.cl
Sent: Wednesday, March 31, 2010 08:55
To: Sumit Gupta
Subject: CCL: Announce: Several MD / QC codes available for GPUs
Sent to CCL by: "Carlos F. Lagos" [cflagos#,#uc.cl]
Is Autodock also available as free code?
-----Mensaje original-----
De: owner-chemistry+carlos==cbuc.cl_._ccl.net
[mailto:owner-chemistry+carlos==cbuc.cl_._ccl.net] En nombre
de Vincent
Leroux
vincent.leroux_+_loria.fr
Enviado el: Martes, 30 de Marzo de 2010 19:25
Para: Lagos, Carlos F
Asunto: CCL: Announce: Several MD / QC codes available for GPUs
Sent to CCL by: Vincent Leroux [vincent.leroux||loria.fr]
Hi,
I have one question.
When will the 3D vision drivers be available under Linux?
Thanks in advance
VL
Le 30/03/10 19:57, Sumit Gupta sugupta^-^nvidia.com a écrit :
> Sent to CCL by: "Sumit Gupta" [sugupta/a\nvidia.com]
> Dear CCL community,
>
> We are happy to announce that several molecular dynamics and quantum
chemistry software are now available on GPUs. These are listed at:
> http://www.nvidia.com/object/tesla_bio_workbench.html
>
> The software includes AMBER, ABINIT (based on BigDFT), ACEMD, GROMACS,
GROMOS,
> HOOMD, LAMMPS, NAMD, TeraChem, VMD. For docking, the HEX
protein-protein
> docking software is available too.
>
> Some of these like ABINIT, GROMOS, and HEX are still not linked from the
link
> above but can be found at:
> ABINIT http://www.abinit.org/ uses BigDFT
http://inac.cea.fr/L_Sim/BigDFT/
> GROMOS http://code.google.com/p/gpugromos/
> HEX http://www.loria.fr/~ritchied/hex/
>
> Please feel free to contact me if you have questions.
>
> Regards
> Sumit
> sumitg AT nvidia com
>
>
>
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<br><font size=2 face="sans-serif">Dear
Colleagues,</font>
<br>
<br><font size=2 face="sans-serif">eHits docking software
have been available
at GPUs for year:</font>
<br>
<br><font size=2 face="sans-serif">http://www.simbiosys.ca/whatsnew/news/index.html#20080424</font>;
<br>
<br><font size=2 face="sans-serif">Best wishes and Happy
Easter!</font>
<br>
<br><font size=2 face="sans-serif">Dr. András
Péter Borosy<br>
Scientific Modelling Expert<br>
<br>
Fragrance Research<br>
Givaudan Schweiz AG - Ueberlandstrasse 138 -
CH-8600
- Dübendorf - Switzerland<br>
T:+41-44-824 2164 - F:+41-44-8242926 -
http://www.givaudan.com</font>
<br>
<br>
<br>
<br>
<table width=100%>
<tr valign=top>
<td width=40%><font size=1
face="sans-serif"><b>"Sumit Gupta
sugupta]~[nvidia.com"
<owner-chemistry#,#ccl.net></b> </font>
<br><font size=1 face="sans-serif">Sent by:
owner-chemistry+andras.borosy==givaudan.com#,#ccl.net</font>
<p><font size=1 face="sans-serif">31.03.2010
21:44</font>
<table border>
<tr valign=top>
<td bgcolor=white>
<div align=center><font size=1 face="sans-serif">Please
respond to<br>
"CCL Subscribers"
<chemistry#,#ccl.net></font></div></table>
<br>
<td width=59%>
<table width=100%>
<tr valign=top>
<td>
<div align=right><font size=1
face="sans-serif">To</font></div>
<td><font size=1 face="sans-serif">"Borosy,
Andras "
<andras.borosy#,#givaudan.com></font>
<tr valign=top>
<td>
<div align=right><font size=1
face="sans-serif">cc</font></div>
<td>
<tr valign=top>
<td>
<div align=right><font size=1
face="sans-serif">Subject</font></div>
<td><font size=1 face="sans-serif">CCL: Announce: Several
MD / QC codes
available for GPUs</font></table>
<br>
<table>
<tr valign=top>
<td>
<td></table>
<br></table>
<br>
<br>
<br><tt><font size=2><br>
Sent to CCL by: Sumit Gupta [sugupta:nvidia.com]<br>
There is an early partial port of AutoDock:<br>
http://sourceforge.net/projects/gpuautodock/<br>;
<br>
There is one more effort to port AutoDock from HCL Infosystems (they<br>
are looking for customers interested in this port).<br>
<br>
Earlier work on AutoDock has shown a healthy speedup<br>
http://www.siliconinformatics.com/products.html<br>;
But this company is no longer marketing AutoDock.<br>
<br>
There are also efforts to port Dock as well (again looking for<br>
potential users).<br>
<br>
A Japanese group (Akiyama et al) out of Tokyo Tech has ported <br>
MegaDock protein-to-protein docking to CUDA.<br>
http://research.microsoft.com/en-us/events/ersymposium2009/accelerated_clusters_proteomics_2.pdf<br>;
<br>
Sumit<br>
----<br>
Sumit Gupta<br>
Sr. Manager - Tesla GPU HPC Group<br>
NVIDIA<br>
<br>
<br>
<br>
-----Original Message-----<br>
> From: owner-chemistry+sugupta==nvidia.com\a/ccl.net [mailto:owner-chemistry+sugupta==nvidia.com\a/ccl.net]
On Behalf Of Carlos F. Lagos cflagos-,-uc.cl<br>
Sent: Wednesday, March 31, 2010 08:55<br>
To: Sumit Gupta<br>
Subject: CCL: Announce: Several MD / QC codes available for GPUs<br>
<br>
<br>
Sent to CCL by: "Carlos F. Lagos" [cflagos#,#uc.cl]<br>
Is Autodock also available as free code? <br>
<br>
-----Mensaje original-----<br>
De: owner-chemistry+carlos==cbuc.cl_._ccl.net<br>
[mailto:owner-chemistry+carlos==cbuc.cl_._ccl.net] En nombre
de Vincent
Leroux<br>
vincent.leroux_+_loria.fr<br>
Enviado el: Martes, 30 de Marzo de 2010 19:25<br>
Para: Lagos, Carlos F <br>
Asunto: CCL: Announce: Several MD / QC codes available for GPUs<br>
<br>
<br>
Sent to CCL by: Vincent Leroux [vincent.leroux||loria.fr]<br>
Hi,<br>
<br>
I have one question.<br>
<br>
When will the 3D vision drivers be available under Linux?<br>
<br>
Thanks in advance<br>
VL<br>
<br>
<br>
<br>
Le 30/03/10 19:57, Sumit Gupta sugupta^-^nvidia.com a écrit :<br>
> Sent to CCL by: "Sumit Gupta"
[sugupta/a\nvidia.com]<br>
> Dear CCL community,<br>
> <br>
> We are happy to announce that several molecular dynamics and
quantum<br>
chemistry software are now available on GPUs. These are listed
at:<br>
> http://www.nvidia.com/object/tesla_bio_workbench.html<br>;
> <br>
> The software includes AMBER, ABINIT (based on BigDFT), ACEMD,
GROMACS,<br>
GROMOS, <br>
> HOOMD, LAMMPS, NAMD, TeraChem, VMD. For docking, the HEX
protein-protein<br>
<br>
> docking software is available too.<br>
> <br>
> Some of these like ABINIT, GROMOS, and HEX are still not linked from
the<br>
link <br>
> above but can be found at:<br>
> ABINIT http://www.abinit.org/ uses BigDFT<br>
http://inac.cea.fr/L_Sim/BigDFT/<br>;
> GROMOS http://code.google.com/p/gpugromos/<br>;
> HEX http://www.loria.fr/~ritchied/hex/<br>;
> <br>
> Please feel free to contact me if you have questions.<br>
> <br>
> Regards<br>
> Sumit<br>
> sumitg AT nvidia com<br>
> <br>
> <br>
><br>
<br>
<br>
<br>
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