PC for Modeling Protein and Drug Interaction

[0dd1ti3]

Hi all,

I'm new. Just created account. I am a researcher starting a new position modeling proteins and drug interactions. I currently have a 2014 13'' macbook pro that I use for data analysis and basic image processing and I will have access to a cluster for more complex work (have to pay by hour). I am looking to build or buy a new PC workstation for more intensive work at home - I've convinced myself that the laptop won't cut it based on how it handles larger photoshop/adobe projects. I have built PCs before switching to Mac for my previous position, but this was a decade ago. It will primarily be for work. I do not game. Ideally, I would want to keep the cost less than $1000 but if that is unrealistic, I can go higher. The lab currently uses Dell Workstations for similar small jobs and just let it run for hours or lets it go overnight - i would like to shorten that for efficiency.

Questions:
1. Is anyone out there involved in similar work and can make a recommendation?

2. I'm leaning towards building my own, but are there any pre-configured PCs that can perform well for 3d rendering/modeling that are worth it?

3. I have heard very good things about AMDs FX series and a friend recommended the FX-8370. Looking online, I see several recommend the AMDs over the Intel i7 and vice versa. Most of the programs I will use do not appear to support hyperthreading. I'm leaning toward the FX-8370. I know the new Zen chips are coming soon, but I would probably still purchase an older chip to take advantage of the price. Good idea?

4. What graphics cards and motherboards should I consider?

Thanks for your help.

 

[ComputerSecurityGuy]

The FX series is really showing its age these days. If you're doing that sort of work, my understanding is that it's heavily threaded. I would pick up an i7 or Xeon, or if it's GPU accelerated spend a bunch on a high end GPU (1070 or 1080). Without knowing what specific software you are using I can't know for sure though.

 

[kanewolf]

For anyone to recommend something, we need to know what the baseline "Dell workstation" that "run for hours" on a job has for a configuration. If that Dell has two Xeons and uses a Tesla card, then we would have difficulty recommending a config for less than thousands of dollars.

 

[0dd1ti3]

Hi all,

Sorry for the delay, but i didn’t want to respond until i got more info. Job start date got pushed back and was just able to confirm.

First, the programs I will need run best on linux. So my OS will need to be linux, but I will probably set up a second hard drive for windows.

The current machine being used is a Dell Optiplex 760.
CPU: Core 2 duo, ≈ 3 GHZ
RAM: 16 Gb
Graphics: Integrated, no discrete card
OS: CentOS
Software: Phenix, Pymol, Coot, Auto Dock Tools

It looks like my options have opened up and i do not need a high end processor, but would like to invest more in RAM and a graphics card. The resolution will benefit from a discrete card and I will need to do occasional video rendering/editting. It will not be used for gaming. Budget is flexible, but would prefer to keep it less than $1000 all in.

So, updated questions:
Recommended Processor?
Recommended Card?
Buy or Build?

Thanks for your input. I appreciate it.

 

[kanewolf]

OK, well Pymol will support NVIDIA 3D display so I would recommend an NVIDIA graphics card. There are articles that say parts of Phenix only scale to 5 cores. So a 6 core would maximize performance. I would get an X99 motherboard (quad channel memory), an i7-5820K (6 cores + hyperthreading), 32 GB RAM (4 x 8GB) and an NVIDIA 1060 (stereo support), 120 or 144 hz monitor for stereo support.

Depending on how you feel about buying used hardware, you can probably find an HP Z800 or Z820 workstation with 8 cores and a Quattro card.

 

[0dd1ti3]

thanks for the input kanewolf. I've built a list on PCpartpicker and will see if any items go on sale this week.

I looked into refurbished workstations and found a few on newegg.com that seem like a good value. They have several z800/z820s with dual Xeon e5-2670 processors. I like them, but have two questions for this route:

1. The ones I see have a Nvidia Quadro 2000 gpu. I understand when this came out, it was a decent mid-range gpu for workstations. Does it matter if a workstation has a workstation GPU or can I upgrade it to a Nvidia 1060?

2. Is having a dual processor system an issue for the 1060?

3. Budget aside, is the dual Xeon a better route than the 5280K?

I really appreciate the input.

 

[kanewolf]

You will end up with more cores and you will have more RAM expandability. You will get slower RAM. But a lot more cache on the CPU. It is probably a better route, since some parts of Pymol will scale to 8+ cores. I would see how the Quadro works before replacing it. You can upgrade to a 1060 but I wouldn't mix a Quadro and non-Quadro. Dual socket is not a problem for a 1060.