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本帖最后由 金鹏 于 2016-5-4 20:02 编辑
接到11704包,在0.017内核下(关闭了PME)跑出的PPD中规中矩. 好怀念0.016内核下的超高PPD
p11706 and p11707 moving to FAH11706:
Here we are simulating the NSD2 protein methyltransferase, a continuation of the Chodera Lab effort to map the conformational landscapes of all protein lysine methyltransferases - important epigenetic enzymes. This will provide powerful data for validations of existing chemical probes and inhibitors of this protein class, as well as will facilitate new explorations of the chemical space for further drug candidates.
NSD2's mutations and chromosomal translocations are implicated in reorganizing the epigenetic landscape in cancers such as multiple myelomas and pediatric acute lymphoblastic leukemia. [doi:10.1016/j.molcel.2011.08.042; doi:10.1038/ng.2777; doi:/10.1371/journal.pgen.1004566].
On interesting things about the simulation - we're continuing using the 4-dummy atom zinc atom model [http://www.mayo.edu/research/lab ... -atom-cada-approach] to model structural zinc clusters in these proteins.
Stats:
# atoms: 62560
credit: 21503
k-factor: 0.75
timeout: 7d
deadline: 10d
Mixed precision calculations are enforced (DP for motion integrations, SP for force calculations). All GPUs lacking DP support are excluded.
11707:
Stats:
# atoms: 35200
credit: 15965
k-factor: 0.75
timeout: 7d
deadline: 10d
11707: Protein lysine methyltransferase SETD8, we have used Ensembler (http://ensembler.readthedocs.org/en/latest/) to generate models from all chains in all available crystal structures - 23 in total. This is the same protein as project 10478, where we started only from two conformations. While I’m analyzing the 1ms (very nice!) of data we’ve gathered there, we’re starting this also with more heterogenous initial conformation seeding. This is part of a bigger ‘operation SETD8’ - next project coming will be a study of this protein in all states of its catalytic cycle to understand changes it undergoes during enzymatic activity and binding of other species.
We have 23 RUNs here, mixed precision is enforced (no-DP GPUs excluded).
Happy Folding! Thanks! 11706 released to ADVANCEDHere we are simulating the NSD2 protein methyltransferase, a continuation of the Chodera Lab effort to map the conformational landscapes of all protein lysine methyltransferases - important epigenetic enzymes. This will provide powerful data for validations of existing chemical probes and inhibitors of this protein class, as well as will facilitate new explorations of the chemical space for further drug candidates.
NSD2's mutations and chromosomal translocations are implicated in reorganizing the epigenetic landscape in cancers such as multiple myelomas and pediatric acute lymphoblastic leukemia. [doi:10.1016/j.molcel.2011.08.042; doi:10.1038/ng.2777; doi:/10.1371/journal.pgen.1004566].
On interesting things about the simulation - we're continuing using the 4-dummy atom zinc atom model [http://www.mayo.edu/research/lab ... -atom-cada-approach] to model structural zinc clusters in these proteins.
Stats:
# atoms: 62560
credit: 21503
k-factor: 0.75
timeout: 7d
deadline: 10d
Mixed precision calculations are enforced (DP for motion integrations, SP for force calculations). All GPUs lacking DP support are excluded. Project 11707 [core21, GPU, LIN/WIN]11707 joining BETA!
Stats:
# atoms: 35200
credit: 15965
k-factor: 0.75
timeout: 7d
deadline: 10d
11707: Protein lysine methyltransferase SETD8, we have used Ensembler (http://ensembler.readthedocs.org/en/latest/) to generate models from all chains in all available crystal structures - 23 in total. This is the same protein as project 10478, where we started only from two conformations. While I’m analyzing the 1ms (very nice!) of data we’ve gathered there, we’re starting this also with more heterogenous initial conformation seeding. This is part of a bigger ‘operation SETD8’ - next project coming will be a study of this protein in all states of its catalytic cycle to understand changes it undergoes during enzymatic activity and binding of other species.
We have 23 RUNs here, mixed precision is enforced (no-DP GPUs excluded).
Thanks everyone for testing! Project 11706 [core21, GPU, LIN/WIN]Project 11706 is finishing it's time in INTERNAL and will be moving into BETA on Wed, April 6th, 11am EST.
Here we are simulating the NSD2 protein methyltransferase, a continuation of the Chodera Lab effort to map the conformational landscapes of all protein lysine methyltransferases - important epigenetic enzymes. This will provide powerful data for validations of existing chemical probes and inhibitors of this protein class, as well as will facilitate new explorations of the chemical space for further drug candidates.
NSD2's mutations and chromosomal translocations are implicated in reorganizing the epigenetic landscape in cancers such as multiple myelomas and pediatric acute lymphoblastic leukemia. [doi:10.1016/j.molcel.2011.08.042; doi:10.1038/ng.2777; doi:/10.1371/journal.pgen.1004566].
On interesting things about the simulation - we're continuing using the 4-dummy atom zinc atom model [http://www.mayo.edu/research/labs/computer-aided-molecular-design/projects/zinc-protein-simulations-using-cationic-dummy-atom-cada-approach] to model structural zinc clusters in these proteins.
Stats:
# atoms: 62560
credit: 21503
k-factor: 0.75
timeout: 7d
deadline: 10d
Mixed precision calculations are enforced (DP for motion integrations, SP for force calculations). All GPUs lacking DP support should be excluded. Assignment Server is running the following constraints:
CODE: SELECT ALLGPU!=None
(
[OS=Linux]
[OS=Win32 CPU=AMD64 OSSpecies != WIN_XP]
)
(
[GPU=NVIDIA GPUSpecies>=2]
[GPU=ATI GPUSpecies>=5]
)
MaxPacket>5
Thanks to everyone for your contributions! Projects 11703-5 [core21, GPU, LIN/WIN] moving to AdvancedProjects 11703, 11704, 11705 moving into ADV!
These are simulations of epigenetic enzymes - protein lysine methyltransferases NSD1 (11703), NSD3 (11704) and SETD2 (11705) using a new multisite Zn2+ ion model.
Stats:
k-factor is 0.75 for all of them
Project 11703
base credit: 24051
timeout: 7d
deadline: 10d
atoms: 68556
Project 11704
base credit: 17402
timeout: 7d
deadline: 10d
atoms: 52855
Project 11705
base credit: 20645
timeout: 7d
deadline: 10d
atoms: 61463
Thanks a lot everyone! Projects 11703-5 [core21, GPU, LIN/WIN]Projects 11703, 11704, 11705 now in beta!
These are simulations of protein lysine methyltransferases NSD1 (11703), NSD3 (11704) and SETD2 (11705) using a new multisite Zn2+ ion model. Note that 11703 and 11704 are replacing 11700 and 11701, which were previously in beta but have been deprecated due to an equilibration / stability issue.
Stats:
k-factor is 0.75 for all of them
Project 11703
base credit: 24051
timeout: 7d
deadline: 10d
Project 11704
base credit: 17402
timeout: 7d
deadline: 10d
Project 11705
base credit: 20645
timeout: 7d
deadline: 10d
Thanks a lot for testing!
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发表于 2016-1-9 09:13:21
