AW: GPU configuration suggestions

From: Norman Geist (
Date: Tue Mar 22 2016 - 02:28:40 CDT


Von: [] Im Auftrag von Nikhil Maroli
Gesendet: Dienstag, 22. März 2016 06:52
Betreff: namd-l: GPU configuration suggestions


Dear all,

we would like to purchase one GPU enabled workstation system for molecular dynamics work,we will be running mainly GROMACS, NAMD and CHARMM (older version which do not support GPU)

i welcome suggestions regarding the below configurations

kindly provide your valued suggestions

Like regarding HDD should i go for SAS,SSD or 7.2k or 10k rpm HDD ?!

You should take more importance on the capacity than the performance. For the MD itself, unless you want to write every step to the trajectory, the HDD speed isn’t critical. So you might go for multiple cheaper e.g. 2TB HDDs and set up a software raid. This will give you good performance, high capacity and also higher availability.

regarding RAM for MD 64 GB is sufficient? (in general we will be working on membrane protein simulations , some time protein folding too)


You never know, but usually NAMD won’t even take half of it even for very large systems.


here is the configuration:

 Processor : 2 x Intel® Xeon® E5-2697 v3 (2.6 GHz, 35 MB cache, 14 cores, Intel® vPro™)
 Chipset : Intel® C612
 RAM : 64GB DDR4-2133 ECC Registered RAM
 Hard disk : 1 TB SATA SSD+ 2 TB SATA (7200 rpm) :OS must installed in SSD partition information as below


Again, I don’t see any benefit from the SSD, especially on a linux system. As you want to do MD, you won’ turn of the machine. And the main benefit why people want to sell you a SSD it the faster booting speed, that few seconds nobody cares about on a linux which will run for weeks.

 Graphics Card : NVIDIA Quadro K2200


Why the expensive Quadro over a comparable GeForce?

 GPU : NVIDIA Tesla K40


Nice, I’d like to have one of these too =)

 Others: Integrated Intel I210AT PCIe GbE; Integrated Intel I218LM PCIe GbE
          Intel 7260 802.11a/b/g/n PCIe WLAN

Nikhil Maroli

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