Dear Dr. Watkins!
Thank you for the suggestions!
In the local shops I've found only Core i7 with 6 cores (like Core
i7-39xx) and 4 cores. Should I obtain much better performance with 6 cores
than with 4 cores in case of i7 cpu (assuming that I run simulation in
cpu+gpu mode )?
Also you've ment
More RAM the better, and the best I have seen is 4 GPU work station. I can use/have used 4. The GPU takes 2 slots though, so a 7-8 PCIe board is really 3-4 GPU, except the tyan mentioned (there designed as blades so an 8 or 10 slot board really holds 8 or 10 GPU's). There's cooling problems tho
I've been running on my Universities GPU nodes these are one E5-xeon (6-cores
12 threads) and have 4 Nvidia 690gtx's. My system is 93 000 atoms of DMF under
NVE. The performance has been a little disappointing ~10ns/day. On my home
system using a core i5-2500 and a nvidia 560ti I get 5.4ns/day
Richard,
thanks for suggestion!
Assuming that I'm using 2 high end GeForce's what performance be better
1) in case of one i7 (4 or 6 nodes ) ?
2) in case of 8 core Xeon like CPU Intel Xeon E5-2650 2.0 GHz / 8core
What properties of MB should take into account primarily for such
Xenon-based sy
Id go for the i7 6 core,
To the other message, funny. I bought ATI's as they clock faster and cost 1/3 the price of Nvidia's but then the software all went to Nvidia. The new ATI with twice the shaders runs at the same speed (around 1-1.3 terflops ) due to the same problems the Nvidias ran
You can also look at profilling on varied web sites, the high end Nvidia run only slightly better than the 2 year old ones, from an individual point not worth the money yet, but if you have the money? as I've been browsing.
Also, the sim I did on the cluster was 180-190,000 atoms so the exac
With the verlet cutoff scheme (new in 4.6) you get much better control
over the drift caused by (missed) short range interactions; you just
set a maximum allowed target drift and the buffer will be calculated
accordingly. Additionally, with the verlet scheme you are free to
tweak the neighbor searc
Of course, you can simulate what you like, but I would personally use an
all-atom representation for long hydrocarbons. I think explicit hydrogens
matter for conformations.
V.V. Chaban
On Thu, May 23, 2013 at 5:16 PM, Bao Kai wrote:
> Hi, all,
>
> I finally wrote a decane topology file. I u
Hello,
I am simulating a lipid bilayer and wish to apply position restraints to
only a subset of the lipids in the bilayer. Since position restraints are
applied to all molecules of the same molecule type, I defined a new
molecule type (DOPR) which is identical to my lipid species (DOPC) by
copyin
AFAIK, the residue names in the mdrun output .gro file are those of the
structure file you gave to grompp.
Mark
On Sun, May 26, 2013 at 12:31 AM, Reid Van Lehn wrote:
> Hello,
>
> I am simulating a lipid bilayer and wish to apply position restraints to
> only a subset of the lipids in the bila
No, the residue names are the those from the .top file. But that's not the
same as the moleculetypes. You have to change the residue names in the [
atoms ] section.
Cheers,
Tsjerk
On Sun, May 26, 2013 at 12:57 AM, Mark Abraham wrote:
> AFAIK, the residue names in the mdrun output .gro file are
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