From owner-chemistry@ccl.net Tue Aug 11 22:08:00 2015 From: "Jiabo Li jiaboli,+,yahoo.com" To: CCL Subject: CCL:G: GPU enabled Computational Software Message-Id: <-51575-150811211823-3952-O64rvfYEsA6Vqd+Asfe9iw[#]server.ccl.net> X-Original-From: Jiabo Li Content-Type: multipart/alternative; boundary="----=_Part_3250586_1899050327.1439342092736" Date: Wed, 12 Aug 2015 01:14:52 +0000 (UTC) MIME-Version: 1.0 Sent to CCL by: Jiabo Li [jiaboli#yahoo.com] ------=_Part_3250586_1899050327.1439342092736 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: quoted-printable Thanks to Mark for a comprehensive list of GPU accelerated computational ch= emistry programs.=C2=A0To complete this list, I would like to a relative ne= wer one: gWEGA: GPU-accelerated WEGA for molecular superposition and shape compariso= n, J. Comp. Chem. 35(2014)1122.=20 WEGA stands for Weighted Gaussian Algorithm for efficient and accurate mole= cular shape comparison. =20 On Tuesday, August 11, 2015 1:53 PM, MARK mark94025/./comcast.net wrote: =20 After further mature reflection, I thought I'd send the actual list of GPU= -accelerated MD, QC, docking and viz progrems. =C2=A0See below: GPU-accelerated quantum chemistry codes are:=C2=A0AbinitACES IIIADFBigDFTCP= 2KGAMESSGAMESS-UKGaussian (in development via OpenACC)GPAWLATTEMOLCASMOPAC2= 013NWChemOCTOPUSQ-CHEMQuantum Espresso/PWscfQUICKTeraChemVASP=C2=A0GPU-acce= lerated MD programs are:=C2=A0ACEMDAMBER (PMEMD)CHARMMDESMONDESPPesSoFoldin= g%HomeGPUgrid.netGROMACSHALMDHOOMD-BlueLAMMPSNAMDOpenMM=C2=A0Molecular Visu= alization and Docking programs are:=C2=A0AMIRA BINDSURFBUDECore HoppingFast= ROCSInteractive Molecule VisualizerMolegro Virtual DockerPIPER Protein Dock= ingPyMolVEGA ZZVMD > From: "MARK" To: "CCL Subscribers" Sent: Wednesday, July 29, 2015 4:00:14 PM Subject: Re: CCL:G: GPU enabled Computational Software See this link on the NVIDIA website for GPU-accelerated applications:=C2=A0= http://www.nvidia.com/object/gpu-applications.html=C2=A0 Search by molecular dynamics, quantum chemistry, bioinformatics or visualiz= ation and docking Mark BergerSenior Alliance Manager, Life & Material SciencesNVIDIA Corporat= ion > From: "John McKelvey jmmckel.%.gmail.com" To: "Mark Berger " Sent: Wednesday, July 29, 2015 1:59:04 PM Subject: CCL:G: GPU enabled Computational Software There is also MOPAC 2012, I believe.... John McKelvey On Wed, Jul 29, 2015 at 1:16 PM, Kristopher Keipert kwk%iastate.edu wrote: The most full featured is Terachem but it is not free. There is also LIBCCHEM for GAMESS-US. On Wed, Jul 29, 2015 at 10:22 AM, Jim Kress jimkress35-$-gmail.com wrote: In searching, I find a somewhat limited implementation of utilization of GP= Us in Quantum Chemistry software.=C2=A0 Does anyone know what QM/ QC packag= e(s) (excluding Gaussian) have the broadest implementation of GPU accelerat= ion?=C2=A0Thanks.=C2=A0Jim --=20 John McKelvey 545 Legacy Pointe DrO'Fallon, MO 63376 636-294-5302 jmmckel[*]gmail.com ------=_Part_3250586_1899050327.1439342092736 Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable
Thanks to Mark for a comprehensive list of GPU accelerated co= mputational chemistry programs. 
To complete this li= st, I would like to a relative newer one:
=
gWEGA: GPU-accelerated WEGA for molecular superpo= sition and shape comparison, J. Comp. Chem. 35(2014)1122.
WEGA stands for Weighted Gaussian Alg= orithm for efficient and accurate molecular shape comparison.

<= div class=3D"yiv9392589583qtdSeparateBR" id=3D"yui_3_16_0_1_1439341870422_5= 285" style=3D"color: rgb(0, 0, 0); font-family: lucida console, sans-serif;= font-size: 13px; background-color: rgb(255, 255, 255);">

<= /div>
= On Tuesday, August 11, 2015 1:53 PM, MARK mark94025/./comcast.net <owne= r-chemistry-$-ccl.net> wrote:


<= div id=3D"yiv9392589583">
After further mature reflection, I thought= I'd send the actual list of GPU-accelerated MD, QC, docking and viz progre= ms.  See below:

GPU-accelerated q= uantum chemistry codes are:
 
Abinit
ACES III
ADF
BigDFT
CP2K
GAMESS
GAMESS-UK
Gaussian= (in development via OpenACC)
GPAW
LATTE
MOLCAS
MOP= AC2013
NWChem
OCTOPUS
<= span style=3D"color: rgb(31, 73, 125);">Q-CHEM
Quantum Espresso/PWscf=
QUICK
TeraChem
VASP
 
GPU-accelerated MD programs are:
 
=
ACEMD<= /span>
AMBER (PMEMD)
CHARMM
DESMOND
ESPPesSo
<= div style=3D"margin: 0px;">Folding= %Home
GPUgrid.net
GROMACS
HALMD
HOOMD-Blue
LA= MMPS
NAMD
OpenMM
 
Molecular Visualization = and Docking programs are:
 
AMIRA
BINDSURF
Core Hopping
FastROCS
Interactive Molecule Visuali= zer
Molegro Virtual Docker
PIPER Protein Docking
PyMol
VEGA ZZ
VMD

From: "MARK" <mark94025%comcas= t.net>
To: "CCL Subscribers" <chemistry%ccl.= net>
Sent: Wednesday, July 29, 2015 4:00:14 PM<= br clear=3D"none">Subject: Re: CCL:G: GPU enabled Computational Soft= ware

See this link on th= e NVIDIA website for GPU-accelerated applications: http://www.nvidia.com/object/gpu-applications.html&n= bsp;

Search by molecular dynamics, = quantum chemistry, bioinformatics or visualization and docking
Mark Berger
Senior Alliance Manager, = Life & Material Sciences
NVIDIA Corporation

From: "Joh= n McKelvey jmmckel.%.gmail.com" <owner-chemistry%ccl.net>
To: "Mark Berger " <mark94025%comcast.net>
Sent: Wednesday, July 29, 2015 1:59:04 PM
Subject: CCL:G: GPU enabled Computational Software
<= div>
There is also MOPAC 2012= , I believe....

John = McKelvey
On Wed, Jul 29, 20= 15 at 1:16 PM, Kristopher Keipert kwk%iastate.edu <o= wner-chemistry[*]ccl.net> wrote:
The most full feature= d is Terachem but it is not free.
There is also LIB= CCHEM for GAMESS-US.

On Wed, Jul 29,= 2015 at 10:22 AM, Jim Kress jimkress35-$-gmail.com <o= wner-chemistry-,-ccl.net> wrote:
In searching, I find a somewhat limited implementation of utilization of= GPUs in Quantum Chemistry software.  Does anyone know what QM/ QC pac= kage(s) (excluding Gaussian) have the broadest implementation of GPU accele= ration?
 
Thanks.=
 <= /span>
Jim




--
John McKelvey
545 Legacy Pointe Dr
O'Fal= lon, MO 63376
636-294-5302
jmmckel[*]gmail.com




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