AMBER MD

AMBER MD

AMBER is a key application in molecular dynamics used to simulate biocatalysis and the interaction between drug candidates and protein receptors. An exemplary feature of AMBER is the ability to use NVIDIA GPUs to massively accelerate complex molecular simulations. This substantially enhances sampling efficiency, improves research accuracy, enables more advanced science, and speeds up the research process.

The main driving force behind the AMBER GPU development has been to bring supercomputer power and performance to individual desktops with an economical price, high power efficiency and designed to benefit the widest range of researchers. Z Workstations provides AMBER GPU computing solutions that provide the optimum price performance for AMBER users.

All AMBER systems come preinstalled with the latest version and updates. Each system is fully turnkey and are ready to run out of the box and provide guaranteed performance. This provides a solution for scientists to acquire optimal workstations and clusters for running GPU AMBER (and regular CPU AMBER simulations as well).

The AMBER 18 package builds on AmberTools18 by adding the pmemd program, which resembles the sander (molecular dynamics) code in AmberTools, but provides better performance on multiple CPUs, and dramatic speed improvements on GPUs.

Major new features in AMBER 18 include:

  • Free energy calculations on GPUs
  • GPU support for 12-6-4 ion potentials
  • Domain decomposition for CPU-parallelism
  • Nudged elastic band calculations for pmemd (CPU and partial GPU implementation)
  • Constant redox potential calculations, to supplement constant pH simulations
  • Support and significant performance improvements for the latest Maxwell, Pascal and Volta GPUs from NVIDIA.
  • New pmemd.gem code for advanced force fields, including AMOEBA

All ZWorkstations AMBER systems come pre-installed with the latest version and updates. Each system is fully turnkey and ready to run out of the box to provide guaranteed performance.

Configuration Recommendations

HP Z640

  • 8-Core 2.1GHz Intel Xeon Broadwell E5-2620 v4 [8-cores / 16-threads]
  • 32GB (4x 8GB) of 2400MHz DDR4 ECC Registered RAM
  • 500GB Solid-State Drive
  • NVIDIA GTX 1080Ti 11GB

$3300.00

Customize & Buy

HP Z840

  • Dual 8-Core 2.1GHz Intel Xeon Broadwell E5-2620 v4 [16-cores / 32-threads]
  • 64GB (4x 16GB) of 2400MHz DDR4 ECC Registered RAM
  • 500GB Solid-State Drive
  • NVIDIA GTX 1080Ti 11GB
  • NVIDIA GTX 1080Ti 11GB

$6150.00

Customize & Buy

HP Z8

  • Dual 12 cores, 2.1 GHz base frequency | Intel Xeon Silver 4116
  • 64GB (8x 8GB) of 2666MHz DDR4 ECC Registered Memory
  • 500GB Solid-State Drive
  • NVIDIA GTX 1080Ti 11GB
  • NVIDIA GTX 1080Ti 11GB
  • NVIDIA GTX 1080Ti 11GB

$9675.00

Customize & Buy

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