For data analysis, two workstation computers were used. Both systems boot into Windows 10 (Microsoft) off a 1 TB M.2 drive (Samsung 970 EVO Plus). The first system consists of an I9-9900X processor (Intel), a GeForce GTX 1070 Ti GPU (Nvidia) and 128 GB of DDR4 RAM (Corsair). The second system has an I9-9900K processor (Intel), a GeForce RTX 2070 GPU (Nvidia) and 64 GB of DDR4 RAM (G.Skill Ripjaws). Data were stored on a 4 TB RAID0 array consisting of two 2 TB drives (Samsung) and a 2 TB RAID0 array consisting of two 1 TB Drives (Samsung), respectively. System integration, support and maintenance performed by Nobska Imaging, Inc.
Geforce rtx 2070 gpu
Manufactured by NVIDIA
Sourced in United States
The GeForce RTX 2070 is a high-performance graphics processing unit (GPU) developed by NVIDIA. It features the Turing architecture and is designed to deliver powerful graphics processing capabilities for a variety of applications.
Automatically generated - may contain errors
Lab products found in correlation
2 protocols using geforce rtx 2070 gpu
1
High-Performance Computing for Data Analysis
2
Molecular Dynamics Simulation of Protein-Ligand Complex
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The MD calculations
were performed with Desmond (v6.5; D.E. Shaw Research, USA; Schrödinger)82 using an NVIDIA GeForce RTX 2070 GPU. System
Builder (Schrödinger) was used to prepare the protein–ligand
complex for the simulations. The TIP3P solvent model was applied,83 (link) with an orthorhombic box shape, a buffer padding
of 12 Å, and the OPLS4 force field. Charges were neutralized
with Cl– ions, and NaCl was added at a concentration
of 0.15 M to mimic the physiological conditions. The simulation time
was set to 100 ns, with recording intervals of 25 ps for the trajectories
and 1.2 ps for the energy. The NPT ensemble was chosen, with the temperature
set to 300 K and the pressure to 1.01325 bar. The RESPA integrator
step was 2 fs, and a Nose–Hoover chain thermostat (relaxation
time 1.0 ps) and a Martyna–Tobias–Klein barostat (relaxation
time 2.0 ps) were used. The short-range Coulombic interaction cutoff
radius was set to 9 Å. The system was relaxed with Maestro’s
build-in relaxation protocol before the commencement of the production
run. The obtained results were analyzed using the Simulation Interactions
Diagram tools (Schrödinger).
were performed with Desmond (v6.5; D.E. Shaw Research, USA; Schrödinger)82 using an NVIDIA GeForce RTX 2070 GPU. System
Builder (Schrödinger) was used to prepare the protein–ligand
complex for the simulations. The TIP3P solvent model was applied,83 (link) with an orthorhombic box shape, a buffer padding
of 12 Å, and the OPLS4 force field. Charges were neutralized
with Cl– ions, and NaCl was added at a concentration
of 0.15 M to mimic the physiological conditions. The simulation time
was set to 100 ns, with recording intervals of 25 ps for the trajectories
and 1.2 ps for the energy. The NPT ensemble was chosen, with the temperature
set to 300 K and the pressure to 1.01325 bar. The RESPA integrator
step was 2 fs, and a Nose–Hoover chain thermostat (relaxation
time 1.0 ps) and a Martyna–Tobias–Klein barostat (relaxation
time 2.0 ps) were used. The short-range Coulombic interaction cutoff
radius was set to 9 Å. The system was relaxed with Maestro’s
build-in relaxation protocol before the commencement of the production
run. The obtained results were analyzed using the Simulation Interactions
Diagram tools (Schrödinger).
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