From owner-chemistry@ccl.net Thu Apr 1 08:47:01 2010 From: "Patrick McCarren patrick.mccarren~!~gmail.com" To: CCL Subject: CCL: Announce: Several MD / QC codes available for GPUs Message-Id: <-41568-100401003020-319-PiUtB0nmu9GwcB6mPcZufw\a/server.ccl.net> X-Original-From: Patrick McCarren Content-Type: multipart/alternative; boundary=000e0cd6147cf9f474048324e65c Date: Thu, 1 Apr 2010 00:00:23 -0400 MIME-Version: 1.0 Sent to CCL by: Patrick McCarren [patrick.mccarren*gmail.com] --000e0cd6147cf9f474048324e65c Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Since 3D TVs are the hot topic this year and NVidia has teamed up with Panasonic, will the Nvidia graphics cards be able to interface with the Panasonic built-in emitter system and glasses or would you have to buy the nvidia 3D emitter and glasses (or RealD) on Linux? I saw a Panasonic Viera system with a racing game on a Windows system here in Boston but we won't b= e able to upgrade to Windows 7 or Vista from XP for a while. What sort of stereo is supported with the Panasonic TV? PyMol has quad-buffered stereo and Maestro and ICM have a few different modes. I think there are definitely a lot of people on the list interested in 3D visualization. Thanks, Patrick On Wed, Mar 31, 2010 at 4:59 PM, Igor Filippov Contr igorf],[helix.nih.gov = < owner-chemistry.:.ccl.net> wrote: > > Sent to CCL by: "Igor Filippov [Contr]" [igorf(~)helix.nih.gov] > I'm interested in 3D stereo as well. > Could you tell us (off-list or on-list) what monitors/glasses > nvidia recommends for 3d stereo? > > Igor > > On Wed, 2010-03-31 at 12:51 -0400, Sumit Gupta sugupta_._nvidia.com > wrote: > > Sent to CCL by: Sumit Gupta [sugupta .. nvidia.com] > > Linux drivers for 3D Vision are already available: > > http://www.nvidia.com/object/linux_display_amd64_195.36.15.html > > > > You will need a GPU board with the stereo connector and we currently on= ly > support the Samsung and Viewsonic panels. > > > > Since this topic is of limited interest to the rest of the CCL communit= y, > > can you please send me a note to my nvidia email address. > > > > Sumit > > > > -----Original Message----- > > > From: owner-chemistry+sugupta=3D=3Dnvidia.com.:.ccl.net [mailto: > owner-chemistry+sugupta =3D=3Dnvidia.com.:.ccl= .net] > On Behalf Of Vincent Leroux vincent.leroux_+_loria.fr > > Sent: Tuesday, March 30, 2010 15:25 > > To: Sumit Gupta > > Subject: 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 =E9crit : > > > 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----------------------------------------------------------------------= ------------- > > This email message is for the sole use of the intended recipient(s) and > may contain > > confidential information. Any unauthorized review, use, disclosure or > distribution > > is prohibited. If you are not the intended recipient, please contact t= he > sender by > > reply email and destroy all copies of the original message. > > > -------------------------------------------------------------------------= ---------- > > > > > > > > -=3Dis is automatically added to each message by the mailing script =3D= > > > > > > > -=3D This is automatically added to each message by the mailing script = =3D-> > > --000e0cd6147cf9f474048324e65c Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Since 3D TVs are the hot topic this year and NVidia has teamed up with Pana= sonic, will the Nvidia graphics cards be able to interface with the Panason= ic built-in emitter system and glasses or would you have to buy the nvidia = 3D emitter and glasses (or RealD) on Linux?=A0 I saw a Panasonic Viera syst= em with a racing game on a Windows system here in Boston but we won't b= e able to upgrade to Windows 7 or Vista from XP for a while.=A0 What sort o= f stereo is supported with the Panasonic TV?=A0 PyMol has quad-buffered ste= reo and Maestro and ICM have a few different modes.=A0 I think there are de= finitely a lot of people on the list interested in 3D visualization.=A0 Tha= nks,

Patrick

On Wed, Mar 31, 2010 at 4:59 = PM, Igor Filippov Contr igorf],[helix.nih.= gov <ow= ner-chemistry.:.ccl.net> wrote:

Sent to CCL by: "Igor Filippov [Contr]" [igorf(~)helix.nih.gov]
I'm interested in 3D stereo as well.
Could you tell us (off-list or on-list) what monitors/glasses
nvidia recommends for 3d stereo?

Igor

On Wed, 2010-03-31 at 12:51 -0400, Sumit Gupta sugupta_._nvidia.com
wrote:
> Sent to CCL by: Sumit Gupta [sugupta .. nvidia.com]
> Linux drivers for 3D Vision are already availa= ble:
> http://www.nvidia.com/object/linux_display_amd64_19= 5.36.15.html
>
> You will need a GPU board with the stereo connector and we currently o= nly support the Samsung and Viewsonic panels.
>
> Since this topic is of limited interest to the rest of the CCL communi= ty,
> can you please send me a note to my nvidia email address.
>
> Sumit
>
> -----Original Message-----
> > From: owner-chemistry+sugupta=3D=3Dnvidia.com.:.ccl.net [mailto:owner-chemistry+sugupta=3D=3Dnvidia.com.:.ccl.net] On Behalf Of Vincent Leroux = vincent.leroux_+_loria.fr=
> Sent: Tuesday, March 30, 2010 15:25
> To: Sumit Gupta
> Subject: 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 =E9crit :
> > Sent to CCL by: "Sumit =A0Gupta" [sugupta/a\nvidia.com]
> > Dear CCL community,
> >
> > We are happy to announce that several molecular dynamics and quan= tum chemistry software are now available on GPUs. =A0 These are listed at:<= br> > > http://www.nvidia.com/object/tesla_bio_workbench.html
> >
> > The software includes AMBER, ABINIT (based on BigDFT), ACEMD, GRO= MACS, GROMOS,
> > HOOMD, LAMMPS, NAMD, TeraChem, VMD. =A0 For docking, the HEX prot= ein-protein
> > docking software is available too.
> >
> > Some of these like ABINIT, GROMOS, and HEX are still not linked f= rom the link
> > above but can be found at:
> > ABINIT http:= //www.abinit.org/ =A0uses 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---------------------------------------------= --------------------------------------
> This email message is for the sole use o= f the intended recipient(s) and may contain
> confidential information. =A0Any unauthorized review, use, disclosure = or distribution
> is prohibited. =A0If you are not the intended recipient, please contac= t the sender by
> reply email and destroy all copies of the original message.
> ----------------------------------------------------------------------= -------------
>
>
>
> -=3Dis is automatically added to each message = by the mailing script =3D>
>



-=3D This is automatically added to each message by the mailing scrip= t =3D-

--000e0cd6147cf9f474048324e65c-- From owner-chemistry@ccl.net Thu Apr 1 09:22:01 2010 From: "andras.borosy_+_givaudan.com" To: CCL Subject: CCL: Announce: Several MD / QC codes available for GPUs Message-Id: <-41569-100401063225-2935-y61vv+pQ8sfQ2u9ulwMnXw!^!server.ccl.net> X-Original-From: andras.borosy]*[givaudan.com Content-Type: multipart/alternative; boundary="=_alternative 0036DD2AC12576F8_=" Date: Thu, 1 Apr 2010 11:59:16 +0200 MIME-Version: 1.0 Sent to CCL by: andras.borosy+/-givaudan.com This is a multipart message in MIME format. --=_alternative 0036DD2AC12576F8_= Content-Type: text/plain; charset="ISO-8859-1" Content-Transfer-Encoding: quoted-printable 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. Andr=E1s P=E9ter Borosy Scientific Modelling Expert Fragrance Research Givaudan Schweiz AG - Ueberlandstrasse 138 - CH-8600 - D=FCbendorf -= =20 Switzerland T:+41-44-824 2164 - F:+41-44-8242926 - http://www.givaudan.com "Sumit Gupta sugupta]~[nvidia.com" =20 Sent by: owner-chemistry+andras.borosy=3D=3Dgivaudan.com#,#ccl.net 31.03.2010 21:44 Please respond to "CCL Subscribers" To "Borosy, Andras " 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=20 MegaDock protein-to-protein docking to CUDA. http://research.microsoft.com/en-us/events/ersymposium2009/accelerated=5Fcl= usters=5Fproteomics=5F2.pdf Sumit ---- Sumit Gupta Sr. Manager - Tesla GPU HPC Group NVIDIA -----Original Message----- > From: owner-chemistry+sugupta=3D=3Dnvidia.com\a/ccl.net=20 [mailto:owner-chemistry+sugupta=3D=3Dnvidia.com\a/ccl.net] On Behalf Of Car= los=20 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?=20 -----Mensaje original----- De: owner-chemistry+carlos=3D=3Dcbuc.cl=5F.=5Fccl.net [mailto:owner-chemistry+carlos=3D=3Dcbuc.cl=5F.=5Fccl.net] En nombre de Vin= cent=20 Leroux vincent.leroux=5F+=5Floria.fr Enviado el: Martes, 30 de Marzo de 2010 19:25 Para: Lagos, Carlos F=20 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 =E9crit : > Sent to CCL by: "Sumit Gupta" [sugupta/a\nvidia.com] > Dear CCL community, >=20 > 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=5Fbio=5Fworkbench.html >=20 > The software includes AMBER, ABINIT (based on BigDFT), ACEMD, GROMACS, GROMOS,=20 > HOOMD, LAMMPS, NAMD, TeraChem, VMD. For docking, the HEX=20 protein-protein > docking software is available too. >=20 > Some of these like ABINIT, GROMOS, and HEX are still not linked from the link=20 > above but can be found at: > ABINIT http://www.abinit.org/ uses BigDFT http://inac.cea.fr/L=5FSim/BigDFT/ > GROMOS http://code.google.com/p/gpugromos/ > HEX http://www.loria.fr/~ritchied/hex/ >=20 > Please feel free to contact me if you have questions. >=20 > Regards > Sumit > sumitg AT nvidia com >=20 >=20 > -=3D This is automatically added to each message by the mailing script=20 =3D-http://www.ccl.net/cgi-bin/ccl/send=5Fccl=5FmessageJob:=20 http://www.ccl.net/jobs=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F Informaci=F3n de ESET= NOD32 Antivirus,=20 versi=F3n de la base de firmas de virus 4987 (20100331) =5F=5F=5F=5F=5F=5F=5F=5F=5F=5F ESET NOD32 Antivirus ha comprobado este mensaje. http://www.eset.com =20 =5F=5F=5F=5F=5F=5F=5F=5F=5F=5F Informaci=F3n de ESET NOD32 Antivirus, versi= =F3n de la base de=20 firmas de virus 4987 (20100331) =5F=5F=5F=5F=5F=5F=5F=5F=5F=5F ESET NOD32 Antivirus ha comprobado este mensaje. http://www.eset.com =20 -=3Dis is automatically added to each message by the mailing script =3D=20 Subscribe/Unsubscribe:=20 Job: http://www.ccl.net/jobs=20 ---------------------------------------------------------------------------= -------- This email message is for the sole use of the intended recipient(s) and=20 may contain confidential information. Any unauthorized review, use, disclosure or=20 distribution is prohibited. If you are not the intended recipient, please contact the=20 sender by reply email and destroy all copies of the original message. ---------------------------------------------------------------------------= -------- -=3D This is automatically added to each message by the mailing script =3D-http://www.ccl.net/cgi-bin/ccl/send=5Fccl=5Fmessagehttp://www.ccl.net/cgi-bin/ccl/send=5Fccl=5Fmessage Subscribe/Unsubscribe:=20 http://www.ccl.net/chemistry/sub=5Funsub.shtmlJob: http://www.ccl.net/jobs=20http://www.ccl.net/spammers.txt--=_alternative 0036DD2AC12576F8_= Content-Type: text/html; charset="ISO-8859-1" Content-Transfer-Encoding: quoted-printable
Dear Colleagues,

eHits docking software have been ava= ilable at GPUs for year:

http://www.simbiosys.ca/whatsnew/new= s/index.html#20080424

Best wishes and Happy Easter!

Dr. Andr=E1s P=E9ter Borosy
Scientific Modelling Expert

Fragrance Research
Givaudan Schweiz AG  -  Ueberlandstrasse 138  -  CH-8600  -  D=FCbendorf  -  Switzerland
T:+41-44-824 2164  -  F:+41-44-8242926    -  http:= //www.givaudan.com



"Sumit Gupta sug= upta]~[nvidia.com" <owner-chemistry#,#ccl.net>
Sent by: owner-chemistry+andras.boro= sy=3D=3Dgivaudan.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=5Fcl= usters=5Fproteomics=5F2.pdf

Sumit
----
Sumit Gupta
Sr. Manager - Tesla GPU HPC Group
NVIDIA



-----Original Message-----
> From: owner-chemistry+sugupta=3D=3Dnvidia.com\a/ccl.net [mailto:owner-= chemistry+sugupta=3D=3Dnvidia.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=3D=3Dcbuc.cl=5F.=5Fccl.net
[mailto:owner-chemistry+carlos=3D=3Dcbuc.cl=5F.=5Fccl.net] En nombre de Vin= cent Leroux
vincent.leroux=5F+=5Floria.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 =E9crit :
> 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=5Fbio=5Fworkbench.html
>
> The software includes AMBER, ABINIT (based on BigDFT), ACEMD, GROMACS,=
GROMOS,
> HOOMD, LAMMPS, NAMD, TeraChem, VMD.   For docking, the HEX protei= n-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=5FSim/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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--=_alternative 0036DD2AC12576F8_=-- From owner-chemistry@ccl.net Thu Apr 1 15:04:00 2010 From: "Igor Filippov Contr igorf%helix.nih.gov" To: CCL Subject: CCL: Announce: Several MD / QC codes available for GPUs Message-Id: <-41570-100401101549-16353-Ms/PdcpmMXkvKWOQtTzA7g.@.server.ccl.net> X-Original-From: "Igor Filippov [Contr]" Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="UTF-8" Date: Thu, 01 Apr 2010 10:12:54 -0400 Mime-Version: 1.0 Sent to CCL by: "Igor Filippov [Contr]" [igorf._+_.helix.nih.gov] Good point about xp/linux and not Win7 being the target OS here. I'm only interested in a configuration that will work on Linux I should add. Igor On Thu, 2010-04-01 at 00:00 -0400, Patrick McCarren patrick.mccarren~! ~gmail.com wrote: > Since 3D TVs are the hot topic this year and NVidia has teamed up with > Panasonic, will the Nvidia graphics cards be able to interface with > the Panasonic built-in emitter system and glasses or would you have to > buy the nvidia 3D emitter and glasses (or RealD) on Linux? I saw a > Panasonic Viera system with a racing game on a Windows system here in > Boston but we won't be able to upgrade to Windows 7 or Vista from XP > for a while. What sort of stereo is supported with the Panasonic TV? > PyMol has quad-buffered stereo and Maestro and ICM have a few > different modes. I think there are definitely a lot of people on the > list interested in 3D visualization. Thanks, > > Patrick > > On Wed, Mar 31, 2010 at 4:59 PM, Igor Filippov Contr > igorf],[helix.nih.gov wrote: > > Sent to CCL by: "Igor Filippov > [Contr]" [igorf(~)helix.nih.gov] > I'm interested in 3D stereo as well. > Could you tell us (off-list or on-list) what monitors/glasses > nvidia recommends for 3d stereo? > > Igor > > On Wed, 2010-03-31 at 12:51 -0400, Sumit Gupta > sugupta_._nvidia.com > wrote: > > Sent to CCL by: Sumit Gupta [sugupta .. nvidia.com] > > > Linux drivers for 3D Vision are already available: > > > http://www.nvidia.com/object/linux_display_amd64_195.36.15.html > > > > You will need a GPU board with the stereo connector and we > currently only support the Samsung and Viewsonic panels. > > > > Since this topic is of limited interest to the rest of the > CCL community, > > can you please send me a note to my nvidia email address. > > > > Sumit > > > > > -----Original Message----- > > > From: owner-chemistry+sugupta==nvidia.com.:.ccl.net > [mailto:owner-chemistry+sugupta==nvidia.com.:.ccl.net] On > Behalf Of Vincent Leroux vincent.leroux_+_loria.fr > > Sent: Tuesday, March 30, 2010 15:25 > > > To: Sumit Gupta > > Subject: 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----------------------------------------------------------------------------------- > > > This email message is for the sole use of the intended > recipient(s) and may contain > > confidential information. Any unauthorized review, use, > disclosure or distribution > > is prohibited. If you are not the intended recipient, > please contact the sender by > > reply email and destroy all copies of the original message. > > > ----------------------------------------------------------------------------------- > > > > > > > > > -=is is automatically added to each message by the mailing > script => > > > > > > > -= This is automatically added to each message by the mailing > script =- > > To recover the email address of the author of the message, > please change > E-mail to subscribers: CHEMISTRY-$-ccl.net or use:> > E-mail to administrators: CHEMISTRY-REQUEST-$-ccl.net or use> Conferences: > http://server.ccl.net/chemistry/announcements/conferences/ > > Search Messages: > http://www.ccl.net/chemistry/searchccl/index.shtml> > > > From owner-chemistry@ccl.net Thu Apr 1 15:39:00 2010 From: "sandhya sandhya.kortagere-.-gmail.com" To: CCL Subject: CCL: Announce: Several MD / QC codes available for GPUs Message-Id: <-41571-100401105456-19489-SrDqcA0DjTO4zHRbnOO8ag:-:server.ccl.net> X-Original-From: sandhya Content-Type: multipart/alternative; boundary=000e0cd705acbad2fd04832d9f05 Date: Thu, 1 Apr 2010 10:24:43 -0400 MIME-Version: 1.0 Sent to CCL by: sandhya [sandhya.kortagere,+,gmail.com] --000e0cd705acbad2fd04832d9f05 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Dear Sumit, I have attempted to set up 3D visualization with RHEL 5.1 on Dell 7300 with Zalman 3D monitor (a suggestion from Dell rep). The monitor came with their own customized glasses. The Dell rep suggested nvidia quadro FX 4800 and once i had the system i set up the stereo on the xconfig file. I still can'= t get the stereo to work on linux. Is there any thing else that needs to be set up or is the monitor just not compatible with linux. i read raving reviews about zalman monitors with Windows. I don't think we can get viewsonic monitors anymore (may be on ebay). any thoughts? warm regards, sandhya. On Wed, Mar 31, 2010 at 4:59 PM, Igor Filippov Contr igorf],[helix.nih.gov = < owner-chemistry__ccl.net> wrote: > > Sent to CCL by: "Igor Filippov [Contr]" [igorf(~)helix.nih.gov] > I'm interested in 3D stereo as well. > Could you tell us (off-list or on-list) what monitors/glasses > nvidia recommends for 3d stereo? > > Igor > > On Wed, 2010-03-31 at 12:51 -0400, Sumit Gupta sugupta_._nvidia.com > wrote: > > Sent to CCL by: Sumit Gupta [sugupta .. nvidia.com] > > Linux drivers for 3D Vision are already available: > > http://www.nvidia.com/object/linux_display_amd64_195.36.15.html > > > > You will need a GPU board with the stereo connector and we currently on= ly > support the Samsung and Viewsonic panels. > > > > Since this topic is of limited interest to the rest of the CCL communit= y, > > can you please send me a note to my nvidia email address. > > > > Sumit > > > > -----Original Message----- > > > From: owner-chemistry+sugupta=3D=3Dnvidia.com.:.ccl.net [mailto: > owner-chemistry+sugupta =3D=3Dnvidia.com.:.ccl= .net] > On Behalf Of Vincent Leroux vincent.leroux_+_loria.fr > > Sent: Tuesday, March 30, 2010 15:25 > > To: Sumit Gupta > > Subject: 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 =E9crit : > > > 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----------------------------------------------------------------------= ------------- > > This email message is for the sole use of the intended recipient(s) and > may contain > > confidential information. Any unauthorized review, use, disclosure or > distribution > > is prohibited. If you are not the intended recipient, please contact t= he > sender by > > reply email and destroy all copies of the original message. > > > -------------------------------------------------------------------------= ---------- > > > > > > > > -=3Dis is automatically added to each message by the mailing script =3D= > > > > > > > -=3D This is automatically added to each message by the mailing script = =3D-> > > --=20 warm regards, sandhya. --000e0cd705acbad2fd04832d9f05 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Dear Sumit,

I have attempted to set up 3D visualization with RHEL 5.= 1 on Dell 7300 with Zalman 3D monitor (a suggestion from Dell rep). The mon= itor came with their own customized glasses. The Dell rep suggested nvidia = quadro FX 4800 and once i had the system i set up the stereo on the xconfig= file. I still can't get the stereo to work on linux. Is there any thin= g else that needs to be set up or is the monitor just not compatible with l= inux. i read raving reviews about zalman monitors with Windows. I don't= think we can get viewsonic monitors anymore (may be on ebay). any thoughts= ?

warm regards,
sandhya.


On Wed,= Mar 31, 2010 at 4:59 PM, Igor Filippov Contr igorf],[helix.nih.gov <owner-chemistry__ccl= .net> wrote:

Sent to CCL by: "Igor Filippov [Contr]" [igorf(~)helix.nih.gov]
I'm interested in 3D stereo as well.
Could you tell us (off-list or on-list) what monitors/glasses
nvidia recommends for 3d stereo?

Igor

On Wed, 2010-03-31 at 12:51 -0400, Sumit Gupta sugupta_._nvidia.com
wrote:
> Sent to CCL by: Sumit Gupta [sugupta .. nvidia.com]
> Linux drivers for 3D Vision are already available:
> http://www.nvidia.com/object/linux_display_amd64_19= 5.36.15.html
>
> You will need a GPU board with the stereo connector and we currently o= nly support the Samsung and Viewsonic panels.
>
> Since this topic is of limited interest to the rest of the CCL communi= ty,
> can you please send me a note to my nvidia email address.
>
> Sumit
>
> -----Original Message-----
> > From: owner-chemistry+sugupta=3D=3Dnvidia.com.:.ccl.net [mailto:owner-chemistry+sugupta=3D=3Dnvidia= .com.:.ccl.net] On Behalf = Of Vincent Leroux vincent.leroux_+_loria.fr
> Sent: Tuesday, March 30, 2010 15:25
> To: Sumit Gupta
> Subject: CCL: Announce: Several MD / QC codes available for GPUs
>
>
> Sent to CCL by: Vincent Leroux [vincent.ler= oux||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 =E9crit :
> > Sent to CCL by: "Sumit =A0Gupta" [sugupta/a\nvidia.com]
> > Dear CCL community,
> >
> > We are happy to announce that several molecular dynamics and quan= tum chemistry software are now available on GPUs. =A0 These are listed at:<= br> > > http://www.nvidia.com/object/tesla_bio_workbench.html
> >
> > The software includes AMBER, ABINIT (based on BigDFT), ACEMD, GRO= MACS, GROMOS,
> > HOOMD, LAMMPS, NAMD, TeraChem, VMD. =A0 For docking, the HEX prot= ein-protein
> > docking software is available too.
> >
> > Some of these like ABINIT, GROMOS, and HEX are still not linked f= rom the link
> > above but can be found at:
> > ABINIT http:= //www.abinit.org/ =A0uses 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---------------------------------------------= --------------------------------------
> This email message is for the sole use of the intende= d recipient(s) and may contain
> confidential information. =A0Any unauthorized review, use, disclosure = or distribution
> is prohibited. =A0If you are not the intended recipient, please contac= t the sender by
> reply email and destroy all copies of the original message.
> ----------------------------------------------------------------------= -------------
>
>
>
> -=3Dis is automatically added to each message by the mailin= g script =3D>
>



-=3D This is automatically added to each message by the mailing scrip= t =3D-



--
warm regard= s,
sandhya.
--000e0cd705acbad2fd04832d9f05-- From owner-chemistry@ccl.net Thu Apr 1 16:19:00 2010 From: "Radoslaw Kaminski rkaminski.rk**gmail.com" To: CCL Subject: CCL: Force Field parameters for Zinc and Chlorine Message-Id: <-41572-100401161723-27248-aERxtpUKX4xYXe9TyM+ojQ _ server.ccl.net> X-Original-From: Radoslaw Kaminski Content-Type: multipart/alternative; boundary=00c09ffb550483c3c30483328c34 Date: Thu, 1 Apr 2010 16:17:15 -0400 MIME-Version: 1.0 Sent to CCL by: Radoslaw Kaminski [rkaminski.rk++gmail.com] --00c09ffb550483c3c30483328c34 Content-Type: text/plain; charset=ISO-8859-1 Hi All, Does anybody have an idea where I can found force field parameters for Zn and Cl atoms? In my case the Zn atom is 4-coordinated to two N atoms and two S atoms. The Cl atoms is bound to aromatic phenyl ring. I was trying to use SYBYL/TRIPOS 5.2 or AMBER (as implemented in ADF) but such atoms types are not included there. Thanks for any help in advance. All the best, Radek --00c09ffb550483c3c30483328c34 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Hi All,

Does anybody have an idea where I can found force field para= meters for Zn and Cl atoms? In my case the Zn atom is 4-coordinated to two = N atoms and two S atoms. The Cl atoms is bound to aromatic phenyl ring. I w= as trying to use SYBYL/TRIPOS 5.2 or AMBER (as implemented in ADF) but such= atoms types are not included there.

Thanks for any help in advance.

All the best,

Radek
--00c09ffb550483c3c30483328c34--