T
TWR
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Hi, I need to build a Linux computer for academic research that will run software for protein docking, molecular dynamics (MD) simulations, and free energy calculations such as Schrödinger Maestro, GOLD - Protein Ligand Docking Software, and, AMBER16, , as well as visualizing 3D molecular structures using software like Visual Molecular Dynamics - VMD. I plan to install the CentOS 7 operating system on this computer since I need to use an older version of one of the softwares. I'm having trouble deciding on what parts to buy since this is my first time building a PC and some of the terms I'm coming across are unfamiliar to me. I'd appreciate any help I can get on finding suitable parts!
From what I've read on the software websites, I think the PC needs to support both CUDA and OpenGL. I need an SSD and HDD and 2 monitors, as well as a CD-ROM drive, and 64GB RAM or more, and a lot of storage space. My budget is around $1500 to $3000, so I was recommended to get "a mid-tier threadripper (12/16 core) and a decent GPU (1080 RTX)."
I've pasted below the requirements for the softwares I need copied from their websites:
Maestro: (https://www.schrodinger.com/kb/1460 ; https://www.schrodinger.com/supportedplatforms/ ; https://www.schrodinger.com/desmond#block-3767)
-Graphics card must support OpenGL 2.1 or greater.
-"We strongly recommend running Maestro using a discrete graphics card for optimal performance, though some integrated graphics cards show acceptable performance. Our software has been tested most robustly against multiple generations of NVidia graphics cards."
"The minimum hardware requirements are:
"The list below gives some guidelines and recommendations for the choice of hardware over the requirements listed above.
The minimum requirements are:
"-Disk Space:
-CSD-System software and data, 17 GB (3 GB software, 14 GB data).
-CSD-CrossMiner software and data, 6 GB (300 MB software, 5.7 GB data)
-Minimum recommended RAM: 8 GB
-Graphics card and drivers that support OpenGL version 2
-The graphics drivers in use should support OpenGL 2.1."
"Recommended Specification for Improved Performance
CPU: Improves any aspect of the software that is carrying out calculations, for example a GOLD docking
Disk Access Speed: The greatest performance increase will be seen in any aspect of the software that requires access to large data files, such as ConQuest database searches
RAM: Increased RAM over 8 GB will help when either looking at large datasets or large complex structures, or else when using multiple CSD-System programs at the same time
GPU: A dedicated modern GPU graphics card, such as those available from NVidia or AMD, will improve performance when visualising large complex structures or large packing diagrams"
AMBER: (https://ambermd.org/gpus/recommended_hardware.htm ; https://ambermd.org/gpus16/index.htm)
"The latest version, AMBER 16, runs up to 15X faster on NVIDIA GPUs over CPU-only systems*, enabling users to run biomolecular simulations in hours instead of days."
"GPU accelerated PMEMD has been implemented using CUDA and thus will only run on NVIDIA GPUs at present although we are working on supporting AMD GPUs."
"AMBER Certified Mid-Level Workstation:
• 2x Intel Xeon E5-2620 v4 CPUs
• 2 to 4 x NVIDIA GTX 1080TI, Titan-X [Pascal] or K40/K80/M40/M60/P40//P100/V100
• 64 GB system memory
• CentOS 6 or 7
AMBER Certified Entry-Level Workstation:
• 1x Intel Core i7-4930K CPU
• 1 or 2 x NVIDIA GTX 1080TI or 1070 GPUs
• 32 GB system memory
• CentOS 6 or 7"
VMD: (http://www.ks.uiuc.edu/Training/Workshop/Pittsburgh2013/Requirements.html)
"The full-featured graphics-enabled mode of VMD is the most demanding, and requires an OpenGL-capable graphics accelerator with up-to-date drivers."
"VMD makes full use of multi-core processors and multiple GPUs for acceleration of the most computationally demanding visualization and analysis tasks. Multi-core CPUs accelerate features including interactive molecular dynamics, bond determination, “within” atom selections and derivatives, so-called streamline or field line visualizations, radial distribution functions, and high quality renderings using the built-in Tachyon and OSPRay ray tracing engines. VMD also supports GPU acceleration using CUDA, and takes advantage of both multi16 core CPUs and GPUs for acceleration of electrostatics (i.e. “volmap coulomb”, and “volmap coulombmsm”), implicit ligand sampling (i.e. “volmap ils”), computation of radial distribution functions, quality-of-fit cross correlation calculation for hybrid fitting methods, trajectory clustering analyses, and computation and rendering of molecular orbitals and molecular surfaces, The latest versions of VMD also incorporate a GPU-accelerated batch and interactive versions of the Tachyon ray tracing engine based on NVIDIA OptiX and CUDA."
"Minimum requirements for Linux:
Thanks so much for reading this! I appreciate any help I can get!
From what I've read on the software websites, I think the PC needs to support both CUDA and OpenGL. I need an SSD and HDD and 2 monitors, as well as a CD-ROM drive, and 64GB RAM or more, and a lot of storage space. My budget is around $1500 to $3000, so I was recommended to get "a mid-tier threadripper (12/16 core) and a decent GPU (1080 RTX)."
I've pasted below the requirements for the softwares I need copied from their websites:
Maestro: (https://www.schrodinger.com/kb/1460 ; https://www.schrodinger.com/supportedplatforms/ ; https://www.schrodinger.com/desmond#block-3767)
-Graphics card must support OpenGL 2.1 or greater.
-"We strongly recommend running Maestro using a discrete graphics card for optimal performance, though some integrated graphics cards show acceptable performance. Our software has been tested most robustly against multiple generations of NVidia graphics cards."
"The minimum hardware requirements are:
- x86_64 compatible processor
- 4 GB memory per core
- 18 GB disk space for software installation; 400-500 GB if databases (PDB, BLAST, etc) are also installed
- Network card with a configured network interface
- 16-bit color (for Maestro)
- 60 GB minimum scratch disk space for running jobs
- Graphics card that supports hardware-accelerated OpenGL with 1GB onboard memory and an up-to-date vendor-supplied graphics driver.
- Monitor with a refresh rate of 60 Hz or more and 1280x1024 resolution.
"The list below gives some guidelines and recommendations for the choice of hardware over the requirements listed above.
- Multiple CPUs. Most jobs can be distributed over multiple processors, so the use of a multi-core CPU or a cluster of CPUs, equipped with a queueing system, is recommended to increase throughput.
- Larger CPU cache is recommended, especially for jobs that process large amounts of data, such as Jaguar and QSite. Increasing the L2 or L3 cache size for these jobs is more important than a small increase in CPU speed.
- Faster local disk access is important for jobs that read a lot of data. For example, using SSD, a disk with a higher speed (e.g. 10000 rpm), or a disk array that uses multiple controllers and striping can be beneficial. Distributed Phase database searches are particularly limited by contention for disk access. Jaguar and QSite jobs also perform a lot of IO, so faster disk access is important. Local disks are preferred over networked disks for temporary storage (or for data that is used often) because networked disks are affected by network access, bandwidth, and network traffic.
- Adequate cooling and power supply. Laptops or notebooks are not usually a good choice for large jobs because the cooling and power supply can be inadequate. If you run jobs for a long time, you should consider a power supply with backup, in case of outages."
The minimum requirements are:
"-Disk Space:
-CSD-System software and data, 17 GB (3 GB software, 14 GB data).
-CSD-CrossMiner software and data, 6 GB (300 MB software, 5.7 GB data)
-Minimum recommended RAM: 8 GB
-Graphics card and drivers that support OpenGL version 2
-The graphics drivers in use should support OpenGL 2.1."
"Recommended Specification for Improved Performance
CPU: Improves any aspect of the software that is carrying out calculations, for example a GOLD docking
Disk Access Speed: The greatest performance increase will be seen in any aspect of the software that requires access to large data files, such as ConQuest database searches
RAM: Increased RAM over 8 GB will help when either looking at large datasets or large complex structures, or else when using multiple CSD-System programs at the same time
GPU: A dedicated modern GPU graphics card, such as those available from NVidia or AMD, will improve performance when visualising large complex structures or large packing diagrams"
AMBER: (https://ambermd.org/gpus/recommended_hardware.htm ; https://ambermd.org/gpus16/index.htm)
"The latest version, AMBER 16, runs up to 15X faster on NVIDIA GPUs over CPU-only systems*, enabling users to run biomolecular simulations in hours instead of days."
"GPU accelerated PMEMD has been implemented using CUDA and thus will only run on NVIDIA GPUs at present although we are working on supporting AMD GPUs."
"AMBER Certified Mid-Level Workstation:
• 2x Intel Xeon E5-2620 v4 CPUs
• 2 to 4 x NVIDIA GTX 1080TI, Titan-X [Pascal] or K40/K80/M40/M60/P40//P100/V100
• 64 GB system memory
• CentOS 6 or 7
AMBER Certified Entry-Level Workstation:
• 1x Intel Core i7-4930K CPU
• 1 or 2 x NVIDIA GTX 1080TI or 1070 GPUs
• 32 GB system memory
• CentOS 6 or 7"
VMD: (http://www.ks.uiuc.edu/Training/Workshop/Pittsburgh2013/Requirements.html)
"The full-featured graphics-enabled mode of VMD is the most demanding, and requires an OpenGL-capable graphics accelerator with up-to-date drivers."
"VMD makes full use of multi-core processors and multiple GPUs for acceleration of the most computationally demanding visualization and analysis tasks. Multi-core CPUs accelerate features including interactive molecular dynamics, bond determination, “within” atom selections and derivatives, so-called streamline or field line visualizations, radial distribution functions, and high quality renderings using the built-in Tachyon and OSPRay ray tracing engines. VMD also supports GPU acceleration using CUDA, and takes advantage of both multi16 core CPUs and GPUs for acceleration of electrostatics (i.e. “volmap coulomb”, and “volmap coulombmsm”), implicit ligand sampling (i.e. “volmap ils”), computation of radial distribution functions, quality-of-fit cross correlation calculation for hybrid fitting methods, trajectory clustering analyses, and computation and rendering of molecular orbitals and molecular surfaces, The latest versions of VMD also incorporate a GPU-accelerated batch and interactive versions of the Tachyon ray tracing engine based on NVIDIA OptiX and CUDA."
"Minimum requirements for Linux:
- Operating System: Any reliable Linux distribution released within the last three years.
- Memory: 512 MB RAM
- Processor: Pentium 4 2.4 Ghz CPU (or comparable)
- Graphics card: nVidia Geforce Ti4600, or comparable"
Thanks so much for reading this! I appreciate any help I can get!
