9606-9617 to FAH (NV Core 18)
Posted: Thu May 14, 2015 9:33 pm
Dear FAH,
In molecular dynamics simulation, the system `model` refers to the equation describing the way the atoms in the simulation interact. For this project series we are running a variety of simulations using different combinations of protein and water models in order to evaluate the model-dependent differences in protein folding dynamics and resultant folded structures. Here we are focusing on 6 peptides/proteins: chignolin, trp-cage, bba, villin, ww domain, and homeodomain. Our goal is to determine which models produce the most accurate results.
SPECIFICATIONS
Uniform across projects:
x18 Nvidia GPU
8 runs
100 clones (1 us / clone)
250 gens (4 ns / gen)
10.8 deadline
2.0 timeout
0.75 k-factor
Unique for each project:
project protein natoms base-credit
p9606 chignolin 3575 130
p9607 chignolin 4720 190
p9608 trp-cage 5899 205
p9609 trp-cage 7770 310
p9610 bba 14104 690
p9611 bba 18636 1050
p9612 villin 9821 390
p9613 villin 12906 650
p9614 ww domain 15175 720
p9615 ww domain 20045 1180
p9616 homeodomain 11878 520
p9617 homeodomain 15530 830
Thank you.
In molecular dynamics simulation, the system `model` refers to the equation describing the way the atoms in the simulation interact. For this project series we are running a variety of simulations using different combinations of protein and water models in order to evaluate the model-dependent differences in protein folding dynamics and resultant folded structures. Here we are focusing on 6 peptides/proteins: chignolin, trp-cage, bba, villin, ww domain, and homeodomain. Our goal is to determine which models produce the most accurate results.
SPECIFICATIONS
Uniform across projects:
x18 Nvidia GPU
8 runs
100 clones (1 us / clone)
250 gens (4 ns / gen)
10.8 deadline
2.0 timeout
0.75 k-factor
Unique for each project:
project protein natoms base-credit
p9606 chignolin 3575 130
p9607 chignolin 4720 190
p9608 trp-cage 5899 205
p9609 trp-cage 7770 310
p9610 bba 14104 690
p9611 bba 18636 1050
p9612 villin 9821 390
p9613 villin 12906 650
p9614 ww domain 15175 720
p9615 ww domain 20045 1180
p9616 homeodomain 11878 520
p9617 homeodomain 15530 830
Thank you.