[gmx-users] Workstation configuration advices?

Javier E jluquedisalvo at gmail.com
Fri Nov 10 11:53:56 CET 2017

Dear users and developers,

I am about to acquire a Workstation to mainly run GROMACS. In choosing a
good configuration that fits the budget, I came out with this basic arrange
(from Dell - Precision 7820 Tower):

- Processor: Intel Xeon Gold 6130 2.1 GHz 3.7 GHz Turbo, 16Core 10.4 GT/s 2
UPI, 22MB cache, HT (125W) DDR-2666. Or any other similar of the Intel
Xenon (R) type.

- Graphic card: NVIDIA Quadro P4000, 8GB, 4DP (7x20TB): even if I would
like a Tesla P100, anyone has used Quadro cards or knows about its
acceleration in GROMACS? Also, are Raedon graphic cards compatible/ tested
for GROMACS (I didn't check if they support CUDA).

- Memory 32 GB (2x16 GB or 4x8GB?) It wont be better 16GB of RAM and maybe
18Cores, 20Cores? The price rises very easy when adding only two-four
cores! The same for the graphic card!

- Primary Hard disk: Solid state (SSD) Class 50 of 512 GB. About the
primary hard disk, should it be NVMe or SATA SSDs? I saw that NVMe has much
better I/O communication but since its relative new tech, I don't know if
GROMACS can fully run here, I believe it does. Also, NVMe it doesn't
support RAID (is RAID a must for GROMACS?), and I'm afraid to encounter
basic problems such as not being able to properly install the OS and the
right dependencies/ libraries/ related tools-software.
- Secondary disk: SATA 3.5'' 1TB 7200 rpm.
- Optional: PCoIP Remote Workstation Card. I saw that it can enhance the
lag. My personal laptop is quite old, is this useful?

I'm intended to simulate polyelectrolyte hydrocarbon-polymers, its water
uptake and ion-diffusion, in simulation boxes of a maximum about 10x10x10
nm, but most of the work would be in much smaller dimensions.

Any comments are highly appreciated.
Best regards


*Javier Luque Di Salvo*

Dipartamento di Ingegneria Chimica

Universitá Degli Studi di Palermo
*Viale delle Scienze, Ed. 6*
*90128 PALERMO (PA)*

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