Parallel Quantum Solutions

WHO ARE WE?

Parallel Quantum Solutions (PQS) manufactures parallel computers with integrated software for high-performance computational chemistry. Our offerings have

• an exceptional performance/price ratio • are fully configured for parallel computation straight out of the box. Our current product, the QuantumCube™, is aimed primarily at ab initio modeling, but we also offer semiempirical, molecular mechanics and dynamics methods.

Our software enables the user to optimize chemical structures and transition states and to predict and display (now optionally including 3D Stereo) properties such as molecular orbitals, charge distributions, electrostatic potentials, vibrational modes and to simulate IR, Raman, VCD and NMR spectra.

The high computational demand of ab initio calculations requires parallel processing to achieve reasonably fast turnaround. Our systems, based on personal computer technology, are fully competitive with expensive general purpose parallel computers (see our benchmarks) at a fraction of the cost. They are affordable by individual researchers or small groups.

To ensure reliability, we use only high quality parts and technologies. Our systems come with the PQS suite of programs fully configured and ready to use.

PQS was founded by Peter Pulay, Jon Baker and Krys Wolinski in 1997.

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HARDWARE QuantumCube™ clusters

Jobs involving large molecules, high levels of theory and many hundreds of basis functions are now commonplace. To meet these high demands all QuantumCube™ clusters are preconfigured for parallel operation and, in combination with the PQS software suite and preinstalled user accounts, are ready for use “straight out of the box.” In addition to our own software, the QuantumCubeTM comes with a wide range of freely available open source computational chemistry software which is installed by default, such as the PSI3 program for high accuracy calculations on small molecules and the NAMD parallel dynamics package. We have arrangements with several third-party software vendors to preinstall their programs at no extra charge other than the standard list price of the software. These include:

• ADF/BAND • MolPro • COSMOtherm • Q-Chem • Jaguar • PCModel • Gaussian • Spartan

We will make our best effort to preinstall any other packages you might require.

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QuantumCube™ turnkey computational chemistry clusters are designed for office use. Standard 20 AMP power lines and residential-grade air conditioning are easily sufficient for optimal operation. Large, efficient 80 mm fans used in combination with straight- through air flow design reduce the heat and noise generated by the machines to below office acceptable levels. Its small size, low noise and relatively small heat footprint make the QuantumCube™ an attractive solution for individuals and small groups. All QuantumCube™ systems come preinstalled with a perpetual license to the full suite of PQS software.

FEATURES

QuantumCubeTM clusters are built using two types of chassis: one holding two dual-processor motherboards and the other holding four. With the multi-core processors available today, this gives us a range of from 24 to 96-CPUs per chassis. Larger clusters can be constructed using multiple chassis.

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Each node in the QuantumCubeTM is configured with two 1 or 2 TB enterprise class drives using mirrored and striped RAID. This speeds up scratch disk access during calculations. All other partitions are mirrored for data integrity.

Our standard configuration provides at least 2 GB of memory per CPU, with at least 4 GB per CPU in the advanced configuration.

All QuantumCubeTM clusters are configured with the latest stable Linux OS, currently CentOS 5.5 (which is fully Red Hat Linux compatible) and a full set of Linux utilities, PQS cluster management tools, MPI and PVM parallel environments and the SGE queuing system. Additional queuing systems can be set up on request. All QuantumCube™ systems come preinstalled with a perpetual license to the full suite of PQS software.

A set of customer-specified user accounts is preinstalled, so users can set up and submit jobs minutes after unpacking the unit. PQS cluster management tools simplify common cluster tasks such as powering up/down, adding users, changing passwords, monitoring node activity, managing the system clocks and data backup.

Each QuantumCubeTM is shipped with a 23” LED monitor, keyboard & mouse, a USB backup drive and a gigabit network switch for models with more than two nodes.

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MODEL OVERVIEW

QuantumCubeTM clusters are equipped with up to 384 GB of RAM, 16TB of disk space, mirrored RAID scratch partitions, and up to 96 cores. We offer both Intel- and AMD-based systems incorporating the latest multi-core processors.

# C R D R # C

P A A i P c n s U o U M M o k r d

/ ( e c s t c G e y s l p o o s p B a r c e e ) c k e

(

G ( ( G G Model B H B ) z ) )

QS24-2660C-XW6 24 2.66 48 2 4,000 2 Intel QS24-2930C-XW6 24 2.93 96 4 8,000 2 Intel QS48-2660C-XW6 48 2.66 96 2 8,000 4 Intel QS48-2930C-XW6 48 2.93 192 4 16,000 4 Intel QS32-2000C-OM8 32 2.00 64 2 4,000 2 AMD QS32-2400C-OM8 32 2.40 128 4 8,000 2 AMD QS64-2000C-OM8 64 2.00 128 2 8,000 4 AMD QS64-2400C-OM8 64 2.40 256 4 16,000 4 AMD QS48-1900C-OM12 48 1.90 96 2 4,000 2 AMD QS48-2200C-OM12 48 2.20 192 4 8,000 2 AMD QS96-1900C-OM12 96 1.90 192 2 8,000 4 AMD QS96-2200C-OM12 96 2.20 384 4 16,000 4 AMD

We use the latest available hardware. The hardware specifications above are current at the time of printing. Please check our website www.pqs- chem.com/machines.html for up-to-date information.

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StereoStationTM Workstations

Thanks to recent advances in both monitor and projector technologies, we are now able to offer a new 3D stereo enabled line of workstations - the StereoStationTM. The stereo effect is achieved through the use of active shutter glasses operating at 120Hz refresh rate. The glasses are synchronized with the display, either a projector or a monitor, producing two distinct images, one for each eye. The visual effect is quite breathtaking and is far superior to the earlier technologies of passive polarized and anaglyph (red/blue) glasses. A number of scientific applications which use OpenGl libraries have been capable of displaying stereo images for several years; however the cost of the necessary hardware has until now been prohibitive. Our systems are preconfigured to run the stereo- enabled version of the PQS suite. Stereo-enabled PyMol is also installed. Additionally we offer support in installing third-party applications on our machines.

MODELS StereoStationTM 2 person SS4-2800-I74-W2P

Intended to be used as a small personal workstation, capable of executing serial PQS jobs and stereo visualization of the results for up to 2 people.

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StereoStationTM 10 person SS4-2800-I74-W10P

Intended for a classroom or research environment, capable of executing serial PQS jobs and stereo visualization of the results for up to 10 people.

StereoQuantumStationTM 2 person SS16-2000-OM8-L2P

Intended for use as a large scale workstation or add-on to an existing PQS QuantumCubeTM. A 16-core, 64 GB of memory Linux node, capable of running a large fully parallel PQS calculation. Results can be viewed in stereo by up to 2 people.

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WARRANTY & SUPPORT

We offer a full, 1 year warranty on all hardware components. Should you have any problems, you can either return the affected equipment to us for repair or replacement, or replace components yourself following our instructions. The warranty can be extended to 2 years for an additional 10% of the system price. Within your warranty period we offer phone and email support as well as remote access support (via ssh) if such access is allowed at your site.

PRICING & DISCOUNTS

Prices for QuantumCubeTM systems start at under $10,000, and for StereoStationTM workstations at under $4,000. A 10% discount on QuantumCubeTM and a 5% discount on StereoStationTM models are available for academic institutions. An additional 5% discount will be applied to all customers (academic or industry) who mention this brochure and order by the end of 2011. Please contact us for an official quote either via email: [email protected] or call us toll free at 1-877-291-2527 or (479) 521-5118. For more details see our website at www.pqs-chem.com.

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SOFTWARE

PQS has three main software offerings:

PQS – our flagship, primarily ab initio software suite offering highly efficient, fully parallel implementations of all the major calculational methods along with some features unique to PQS

SQM – an add-on module for scaling ab initio Hessian matrices, providing excellent agreement with experimental vibrational spectra

PQSMol – our graphical user interface which includes a model builder, input preparation, parallel job submission and post-job visualization and display

All PQS software can be purchased inexpensively independently of our hardware.

PRICING

Prices are for an annual license.

Academic PQS: $125 PQSMol: $100 SQM: $40 Industrial PQS: $250 PQSMol: $200 SQM: $80

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PQS Version 4.0 Software Features

• Restricted and unrestricted Hartree-Fock and DFT energies and gradients, including several initial wavefunction guess options • Wide range of exchange-correlation functionals: VWN, B88, OPTX, LYP, P86, PW91, PBE, B97, HCTH, B3LYP, make up your own functional ... • Fast and accurate pure DFT energies and gradients for large basis sets using the FTC method • Efficient geometry optimization for minima and transition states using delocalized internal, Cartesian or Z-matrix coordinates; special coordinates for optimization of molecular clusters • Enforced geometry optimization in the presence of an applied external force • Full range of geometrical constraints including fixed distances, planar bends, torsions and out-of-plane bends between any atoms in the molecule and frozen (fixed) atoms. Atoms involved in constraints do not need to be formally bonded and - unlike with a Z matrix - desired constraints do not need to be satisfied in the starting geometry • Analytical HF and DFT second derivatives including vibrational frequencies, IR and Raman intensities, VCD rotational strengths and thermodynamic analysis • Scaled Quantum Mechanical (SQM) force field • Efficient NMR chemical shifts for closed-shell HF and DFT wavefunctions • Relativistic and non-relativistic ECPs for energies, gradients, second derivatives and NMR

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• Closed-shell MP2 energies and analytical gradients; numerical MP2 second derivatives • Open-shell UMP2 energies and numerical gradients • New correlated energy module with MP3, MP4, CID, CISD, CEPA-0, CEPA-2, QCISD, QCISD(T), CCD, CCSD and CCSD(T) • COSMO solvation model including energies, gradients and numerical second derivatives + NMR • Potential scan, including scan plus optimization of all other variables • Reaction path (IRC) following • Population analysis, including bond orders, atomic valencies and free valencies • Weinhold's natural bond order analysis (NBO 5.0) • Charge/spin density and electric field gradient • Polarizability, hyperpolarizability and polarizability derivatives • Full geometry optimization, NMR and vibrational frequencies in an external electric field • Basis set library with wide range of basis sets, including several ECP bases • Abelian point group symmetry throughout; utilizes full point

group symmetry (up to Ih) for geometry optimization step • Full semiempirical module with MINDO/3, MNDO, AM1 and PM3 • Molecular mechanics with Sybyl 5.0 and UFF force fields • QM/MM using the ONIOM method • Direct molecular dynamics • All major ab initio functionality is fully parallel (except MP2 gradients which is serial only)

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BENCHMARKS

8-CPU job times for a system based on 2.93 GHz 6-core Intel Westmere processors. Format: molecule, time in minutes, symmetry, method/basis [number of basis functions], job type (FREQ=frequency; OPT=optimization (cycles); E=energy; G=gradient; NMR=chemical shift)

• (H2O)20 1.0 min C1 MP2/6-31G** [380] SCF + MP2 • sucrose (C12H22O11) 12.2 min C1 RHF/6-31G** [455] E + FREQ • bucky ball(C60) 19.6 min Ih BLYP/3-21G [540] OPT(8) + FREQ • benzyl-mitomycin(C23H26N4O6) 3.8 min C1 BVP86/SVP [592] COSMO E + G • taxol (C47H51NO14) 4.7 min C1 BVWN/3-21G [660] E + NMR • Si3AlO4(OH)8Cu 9.0 min C1 B3LYP/VTZDP [664] E • (glycine)10 (C20H32N10O11) 5.8 min C1 MP2/6-31G* [679] SCF + MP2 • zinc phthalocyanine (C32H16N8Zn) 1.5 min D4h B3LYP/6-31G** [719] E • yohimbine (C21H26N2O3) 10.3 min C1 OLYP/PC-2 FTC+SEMI [1144] E • chlorophyll (C55H74N4O5Mg) 21.6 min C1 B3LYP/VDZP [1266] E + G • taxol (C47H51NO14) 158.0 min C1 MP2/6-311G** [1422] SCF + MP2 • calix[4]arene (C32H32O4) 68.0 min C2v MP2/cc-pvtz [1528] SCF + MP2

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SQM Version 2.0

Optimizes scale factors for best least-squares fit to known experimental frequencies; scale factors can be transferred to other molecules with similar structural motifs allowing accurate a priori predictions of complete vibrational spectra and checking of experimental assignments.

SQM version 2.0 now includes symmetry assignments of all vibrational modes and a full thermodynamic analysis.

The above shows a comparison of a high-resolution vapor phase FTIR spectrum of toluene with a predicted B3LYP/6-31G* SQM spectrum. The average deviation between the predicted and experimental fundamentals is just 5.3 cm-1. (FTIR spectrum courtesy of Fiveash Data Management.)

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PQSMol Version 2.0

PQSMol is our graphical user interface for constructing molecules, input preparation, job submission and post-job visualization and display. Display options include: molecular orbitals (canonical, local and natural), electron and spin densities, electrostatic potentials, geometries and optimization history, dynamics trajectories, animation of vibrational modes and simulated IR/Raman, VCD and NMR spectra.

New features in version 2.0 include dipole moment display, assignment of constraints for geometry optimization, virtual bonds, geometry distortion along specified vibrational modes, chirality change and 3D stereo display.

The screenshots below show the HOMO (left) and the VCD spectrum (right) for C8H12OFCl, a chiral cyclic fluorochloroketone, computed at the B3LYP/6-31G* level.

Full 3D stereo display now available on our StereoStation™.

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