Folding Forum

Thanks for your response, I don't think I was clear. I was asking how do they build the .pdb which tells the proteins information in 3D (X,Y,Z Coordinates) . Yes the primary structure is a straight line of aa's, but i was asking IF that is what they do to start off the simulation. As for you saying ...

So you guys do not use xray-crystal as I understand from a previous post. What is the starting point of a protein? Is it in its primary structure.

I have been playing around with 5-6 MD programs and I would have to say by far the best has been OpenMM Zephyr. Installation was extremely easy and even an idiot like me can work it!. Anyways, when I was playing around with that program with gpu acceleration, whenever I used implicit solvent my gpu ...

You got it right

Thanks for all the responses. Very interesting, even though I knew it, I am sure others learned something though, so not a waste. I am no expert (just a second year chem student) but from what I am looking up it seems to me I would need the native state, which is why I am interested in this. To Jess...

On the site (http://copernicus-computing.org/) it says "we observe structures 0.6Å from the native state within 30h" and "achieve sufficient sampling to predict the native state without a priori knowledge after 80-90h". Which type and how many processors did you guys use to get t...

I didn't know what section to put this in, so put it here.

Name says it all, when fah6.exe is run why not ask teh user to input the amount of threads to be used?

Would be much more efficient (for me at least) to do that rather than keep on editing the client.cfg file.

I'm not disputing the importance of hands on participation from people themselves, after all, if I didn't start using the unicore client myself, I wouldn't be here today. However, there are pros and cons to each of them, but just because we are given two choices does not mean we have to choose one o...

You bring up good points on ethics of using comparison, but I'll explain why sometimes putting all the facts and details of a subject is detrimental to what I plan to do. Let me explain. So I have a business and I donate money for building a $2100 PC with 4 GTX 560 Ti's and 1 i7-2600. My goal is to ...

Well, I would imagine it would be a quick coding fix, justnothing too complicated. Jut get the SMP client to run a single WU that is designated at the benchmark, and have a complete separate client just for the benchmarking. As for the waste of computations, limit the time frame of simulation so tha...

Hmmm, would be nice to have a "benchmark WU" that takes 5 minutes to finish and reports how many FLOPS the CPU/GPU is capable of. The reason I am so adamant about this is because I need to communicate with numbers (FLOPS) how effective a certain build is. The more FLOPS/$ the better. It is...

I spent extra for the Antex 900 because of cooling, I thought i was generous because it is a $100 case :S As for the depth of the case, It would be a bad day for me if i set that up and found out the 4th gpu didn't fit, i hope they have exact spec for that as it will be a pita to figure out (as wher...

So could there be an estimate on how much x86 FLOPS there are for a GTX 460 Ti? Also how does f@h actually calculate FLOPS? Does it look for hardware IDs to figure out what CPU/GPU they are using and just add the numbers up from active clients, making it a best case scenario if those active clients ...

According to http://en.wikipedia.org/wiki/GeForce_500_Series the GFLOPS of a 560 Ti is 1263.4. I'm assuming these are native FLOPS. and teh conversion from native FLOPS to x86 FLOPS for Nvidea GPUs is 1:2.11 (from http://fah-web.stanford.edu/cgi-bin/main.py?qtype=osstats ) so is it fair to say that ...

Hell, I'd take a trip to Stanford!