BioSimGrid

Trajectory index

Last updated on Mon Jun 16 02:00:01 2008

2lao (BioSimGrid_GB-OXF_2013)
mouse acetylcholinesterase * (BioSimGrid_GB-OXF_11)
mouse acetylcholinesterase (BioSimGrid_GB-OXF_12)
T4 lysozyme (BioSimGrid_GB-OXF_13)
outer-membrane phospholipase A (BioSimGrid_GB-OXF_9)
outer-membrane phospholipase A (BioSimGrid_GB-OXF_17)
OmpA (0.1 M NaCl; 5 ps/10 ns) (BioSimGrid_GB-OXF_29)
OmpX (BioSimGrid_GB-OXF_30)
pindolol (2) (BioSimGrid_GB-OXF_33)
scorpion toxin: 1AGT (BioSimGrid_GB-OXF_42)
scorpion toxin: 1AGT mutant F25A (BioSimGrid_GB-OXF_43)
scorpion toxin: 1AGT mutant G10V (BioSimGrid_GB-OXF_44)
scorpion toxin: 1AGT mutant H34A (BioSimGrid_GB-OXF_45)
scorpion toxin: 1AGT mutant K27M (BioSimGrid_GB-OXF_46)
scorpion toxin: 1AGT mutant K32A (BioSimGrid_GB-OXF_47)
scorpion toxin: 1AGT mutant M29A (BioSimGrid_GB-OXF_48)
scorpion toxin: 1AGT mutant N30A (BioSimGrid_GB-OXF_49)
scorpion toxin: 1AGT mutant P37A (BioSimGrid_GB-OXF_50)
scorpion toxin: 1AGT mutant R24A (BioSimGrid_GB-OXF_51)
scorpion toxin: 1AGT mutant R31A (BioSimGrid_GB-OXF_52)
scorpion toxin: 1AGT mutant S11A (BioSimGrid_GB-OXF_53)
scorpion toxin: 1AGT mutant T36A (BioSimGrid_GB-OXF_54)
scorpion toxin: 1AGT mutant T9A (BioSimGrid_GB-OXF_55)
OprF (Syma, vis) (BioSimGrid_GB-OXF_83)
OmpT, DMPC and water production run (cutoff; short trajectory 1) (BioSimGrid_GB-OXF_91)
OmpT, DMPC and water production run (cutoff) (BioSimGrid_GB-OXF_94)
PagP in POE/POG mixed bilayer (BioSimGrid_GB-OXF_104)
PagP from Og, uncharged His33, bound 192, si (BioSimGrid_GB-OXF_115)
yalini (BioSimGrid_GB-OXF_116)
PagP NMR charged without bound lipid (BioSimGrid_GB-OXF_139)
DMPC bilayer (BioSimGrid_GB-OXF_4)
outer-membrane phospholipase A * (BioSimGrid_GB-OXF_16)
OprF (Syma, tilt) (BioSimGrid_GB-OXF_8)
OmpA (20 ns; no water) (BioSimGrid_GB-OXF_36)
scorpion toxin: 1TXM (BioSimGrid_GB-OXF_76)
scorpion toxin: 2BMT (BioSimGrid_GB-OXF_77)
scorpion toxin: 2KTX (70 ns) (BioSimGrid_GB-OXF_78)
scorpion toxin: 2PTA (BioSimGrid_GB-OXF_79)
PagP (with charges) (BioSimGrid_GB-OXF_88)
Kir6.2i (PDXN; 2 ns to 10 ns) (BioSimGrid_GB-OXF_89)
OmpT, DMPC and water production run (PME) (BioSimGrid_GB-OXF_95)
scorpion toxin: 2KTX (60 ns) (BioSimGrid_GB-OXF_117)
PagP charged in POPC bilayer (BioSimGrid_GB-OXF_136)
Haein (BioSimGrid_GB-OXF_27)
Entae (BioSimGrid_GB-OXF_28)
PagP (without charges) (BioSimGrid_GB-OXF_31)
OpcA (20 ns; 0.1 M NaCl) (BioSimGrid_GB-OXF_34)
NspA (BioSimGrid_GB-OXF_39)
scorpion toxin: 1AHO (BioSimGrid_GB-OXF_56)
scorpion toxin: 1BIG (BioSimGrid_GB-OXF_57)
scorpion toxin: 1BKT (BioSimGrid_GB-OXF_58)
scorpion toxin: 1C49 (BioSimGrid_GB-OXF_59)
scorpion toxin: 1C56 (BioSimGrid_GB-OXF_60)
scorpion toxin: 1DU9 (BioSimGrid_GB-OXF_61)
scorpion toxin: 1HP2 (BioSimGrid_GB-OXF_62)
scorpion toxin: 1HP9 (BioSimGrid_GB-OXF_63)
scorpion toxin: 1J5J (BioSimGrid_GB-OXF_64)
scorpion toxin: 1LIR (BioSimGrid_GB-OXF_65)
scorpion toxin: 1MTX (BioSimGrid_GB-OXF_66)
scorpion toxin: 1NE5 (BioSimGrid_GB-OXF_67)
scorpion toxin: 1PNH (BioSimGrid_GB-OXF_68)
scorpion toxin: 1Q2K (BioSimGrid_GB-OXF_69)
scorpion toxin: 1QUZ (BioSimGrid_GB-OXF_70)
scorpion toxin: 1SCO (BioSimGrid_GB-OXF_71)
scorpion toxin: 1SCY (BioSimGrid_GB-OXF_72)
scorpion toxin: 1SIS (BioSimGrid_GB-OXF_73)
scorpion toxin: 1SXM (BioSimGrid_GB-OXF_74)
scorpion toxin: 1TSK (BioSimGrid_GB-OXF_75)
OmpT, DMPC and water production run (cutoff; short trajectory 2) (BioSimGrid_GB-OXF_92)
OmpT, DMPC and water production run (cutoff; short trajectory 3) (BioSimGrid_GB-OXF_93)
glur0_closed-apo (BioSimGrid_GB-OXF_118)
pagp uncharged in popc bilayer (BioSimGrid_GB-OXF_135)
outer-membrane phospholipase A (BioSimGrid_GB-OXF_10)
outer-membrane phospholipase A (BioSimGrid_GB-OXF_14)
outer-membrane phospholipase A (BioSimGrid_GB-OXF_15)
pindolol (1) (BioSimGrid_GB-OXF_23)
OpcA (20 ns; 1 M NaCl) (BioSimGrid_GB-OXF_38)
scorpion toxin: 1ACW (BioSimGrid_GB-OXF_41)
SecY (2 ns to 15 ns) (BioSimGrid_GB-OXF_90)
OmpT, DMPC and water production run (cutoff; short trajectory 4) (BioSimGrid_GB-OXF_96)
PagP from Og ensemble in DMPC bilayer (deprotonated His) (BioSimGrid_GB-OXF_100)
PagP from Og ensemle (deprotonated His33, s-i pressure coupling) (BioSimGrid_GB-OXF_101)
PagP from Og ensemble, si pressure coupling, deprotonated His33, with 192 (BioSimGrid_GB-OXF_102)
LBP- 1000 frames test (BioSimGrid_GB-OXF_2020)
KcsA in PopE (Sundeep Deol) (BioSimGrid_GB-OXF_3135)
new NAMD trajectory: /home/esther/storage/benzocrown/1+slab+1/namdrunWaterDeposit (BioSimGrid_GB-STH_2717)
Blc and bilayer (BioSimGrid_GB-OXF_2414)
PagP charged in DPPC (BioSimGrid_GB-OXF_154)
apo-AChE (J Kua) (BioSimGrid_GB-STH_1966)
1USG (Leucine Binding Protein) (BioSimGrid_GB-OXF_2065)
PagP PX in OG (BioSimGrid_GB-OXF_141)
PagP uncharged in DPPC (BioSimGrid_GB-OXF_155)
water (64 bzcrown) (BioSimGrid_GB-STH_2820)
KcsA in PopA (Sundeep Deol) (BioSimGrid_GB-OXF_3117)
KcsA in PopG (Sundeep Deol) (BioSimGrid_GB-OXF_3136)
KcsA in mixed bilayer: 167 POPE, 75 POPG (Sundeep Deol) (BioSimGrid_GB-OXF_3137)
Isolated VS of KvAP with ASP147 ionized and simulated at 368K in a DM micelle (BioSimGrid_GB-OXF_3237)
Isolated VS of KvAP with ASP147 ionized and simulated at 300K (BioSimGrid_GB-OXF_3140)
Isolated VS of KvAP with ASP147 protonated and simulated at 300K in a DM micelle (BioSimGrid_GB-OXF_3255)
Isolated VS of KvAP with ASP147 protonated and simulated at 368K in a DM micelle (BioSimGrid_GB-OXF_3256)
PNNL Test Prion trajectory (BioSimGrid_GB-STH_3889)
First PNNL NWCHEM trajectory (BioSimGrid_GB-STH_4096)
equilibrating a fat box of lipid and water (BioSimGrid_GB-STH_4296)
PNNL Test Prion trajectory (BioSimGrid_GB-STH_3890)
equilibrating solvated-inserted Kir2.1 with restraints on the protein (BioSimGrid_GB-STH_4297)
equilibrating solvated-inserted Kir2.1 with alpha-carbon atoms restrained (halved strength to 500 kJ/mol/(nm^2)) (BioSimGrid_GB-OXF_4357)
lipid self-assembly around Kir2.1 for 100 ns (extended from 50 ns) (BioSimGrid_GB-OXF_4456)
lipid self-assembly around Kir2.1 for 100 ns: box size 12 nm cubed; 400 lipid molecules (BioSimGrid_GB-OXF_4477)
lipid self-assembly around Kir2.1: box size 12 nm cubed; 300 lipid molecules (crashed) (BioSimGrid_GB-OXF_4478)
Kir2.1 in lipid bilayer, with backbone and lipid headgroups restrained (BioSimGrid_GB-OXF_4480)
equilibrating solvated-inserted Kir2.1 with nothing restrained and with 1 fs timesteps (BioSimGrid_GB-OXF_4301)
equilibrating solvated-inserted Kir2.1 with alpha-carbon atoms restrained (BioSimGrid_GB-OXF_4316)
equilibrating solvated-inserted Kir2.1 with alpha-carbon atoms restrained (halved strength to 500 kJ/mol/(nm^2)) (BioSimGrid_GB-OXF_4335)
coarse-grain lipid self-assembly around Kir2.1 with 450 lipid molecules for 50 ns (BioSimGrid_GB-OXF_4375)
lipid self-assembly around Kir2.1 with 250 lipid molecules (BioSimGrid_GB-OXF_4398)
lipid self-assembly around Kir2.1 with 350 lipid molecules (BioSimGrid_GB-OXF_4397)
Kir2.1 in lipid bilayer with alpha-carbon atoms restrained and lipid headgroups restrained in the z-direction (BioSimGrid_GB-OXF_4496)
coarse-grain lipid self-assembly around Kir2.1 with 300 lipid molecules and a (12 nm)^3 box (BioSimGrid_GB-OXF_4495)
Kir2.1 in lipid bilayer with alpha-carbon atoms weakly restrained and lipid headgroups weakly restrained in the z-direction (BioSimGrid_GB-OXF_4515)
Kir2.1 in lipid bilayer with no restraints and 1 fs timestep for 1 ns (BioSimGrid_GB-OXF_4535)
Kir2.1 (2 ions in cavity) in lipid bilayer with no restraints and 2 fs timestep for 1 ns (BioSimGrid_GB-OXF_4556)
equilibrating solvated-inserted Kir2.1 with backbone atoms restrained (BioSimGrid_GB-STH_4298)
coarse-grain lipid self-assembly around Kir2.1 (BioSimGrid_GB-OXF_4358)
Kir2.1 equilibration for 1 ns with 1 fs timesteps (BioSimGrid_GB-OXF_4395)
Kir2.1 (3 ions in cavity) in lipid bilayer with no restraints and 2 fs timestep for 1 ns (BioSimGrid_GB-OXF_4557)
Kir2.1 (2 ions in cavity) in lipid bilayer with no restraints and 2 fs timestep for 1 ns (not complete: only a bit more than 0.9 ns) (BioSimGrid_GB-OXF_4559)
Kir2.1 (3 ions in cavity) in lipid bilayer with no restraints and 2 fs timestep for 1 ns (not complete: only a bit more than 0.9 ns) (BioSimGrid_GB-OXF_4560)
Kir2.1 (3 ions in cavity) in lipid bilayer with no restraints and 1 fs timestep (after earlier equilibration for 0.9 ns with 1 fs timestep) (BioSimGrid_GB-OXF_4576)
Magnetospirillum magnetotacticum, Kirbac3.1, full structure (BioSimGrid_GB-OXF_3550)
Kir2.1 in lipid bilayer; production run: prod2 (BioSimGrid_GB-OXF_4757)
Kir2.1 in lipid bilayer; production run (note treatment of termini): prod3 (BioSimGrid_GB-OXF_4775)
Kir2.1 (closed-state chimera-templated) in lipid bilayer; equilibration at 100 K (with restraint on the protein): fixProtein100K (BioSimGrid_GB-OXF_4820)
Kir2.1 production run: prod0 (BioSimGrid_GB-OXF_4595)
Kir2.1 production run: prod1 (BioSimGrid_GB-OXF_4615)
Kir2.1 (3 ions in cavity) in lipid bilayer with distance restraints on the salt bridges behind the filter between Glu138 and Arg148 and 2 fs timestep: saltbridge (BioSimGrid_GB-OXF_4676)
Kir2.1 (closed-state chimera-templated) in lipid bilayer; equilibration at 200 K (no restraints): fixProtein200K (BioSimGrid_GB-OXF_4818) new!
Kir2.1 (closed-state chimera-templated) in lipid bilayer; equilibration at 310 K (no restraints): fixProtein310K (BioSimGrid_GB-OXF_4819)
Kir2.1 (closed-state chimera-templated) in lipid bilayer; equilibration at 200 K (with restraint on the protein): fixProtein200K (BioSimGrid_GB-OXF_4821)
Kir2.1 (closed-state chimera-templated) in lipid bilayer; equilibration at 310 K (with restraint on the protein): fixProtein310K (BioSimGrid_GB-OXF_4822)
Kir2.1 (closed-state chimera-templated) in lipid bilayer; equilibration at 310 K (restraining the backbone atoms): backbone1fs (BioSimGrid_GB-OXF_4823)
Kir2.1 (closed-state chimera-templated) in lipid bilayer; equilibration at 310 K (restraining the alpha-carbon atoms): alpha1fs (BioSimGrid_GB-OXF_4835)
Kir2.1 (closed-state chimera-templated) in lipid bilayer; production run after restrained equilibration (with ion in cavity initially): prod0 (BioSimGrid_GB-OXF_4895)
Kir2.1 (closed-state chimera-templated) in lipid bilayer; production run after restrained equilibration (no ion in cavity initially): KDB S300 'closed'; downsampled from BioSimGrid_GB-OXF_4875, BioSimGrid_GB-OXF_4935, and BioSimGrid_GB-OXF_4997 (BioSimGrid_GB-OXF_5035) new!
Kir2.1 (3 ions in cavity) in lipid bilayer with no restraints and 2 fs timestep (after earlier equilibration for 0.9 ns with 1 fs timestep) (BioSimGrid_GB-OXF_4577)
Kir2.1 (closed-state chimera-templated) in lipid bilayer; equilibration at 100 K (no restraints): fixProtein100K (BioSimGrid_GB-OXF_4817)
Kir2.1 (closed-state chimera-templated) in lipid bilayer; production run after unrestrained equilibration: prod0 (BioSimGrid_GB-OXF_4856)
Kir2.1 (closed-state chimera-templated) in lipid bilayer; production run after unrestrained equilibration: prod2 (BioSimGrid_GB-OXF_4975) new!
Kir2.1 (closed-state chimera-templated) in lipid bilayer; production run after restrained equilibration (with 7 ions in cavity initially): 'crowd' prod0 (0 ns to 10 ns) (BioSimGrid_GB-OXF_5095) new!
Kir2.1 (closed-state chimera-templated) in lipid bilayer; production run after unrestrained equilibration (no ion in cavity initially): KDB S301 'closed_'; downsampled from BioSimGrid_GB-OXF_4856, BioSimGrid_GB-OXF_4915, and BioSimGrid_GB-OXF_4975 (BioSimGrid_GB-OXF_5037) new!
unrestrained 20ns simulation of KcsA in a large POPC bilayer and was run using GROMACS3.3.1. The initial state of the filter was WKWK(K), Glu-71 was protonated, waters were added to the cavity of the channel and waters were placed behind the pore helices. (BioSimGrid_GB-OXF_4635)
Kir2.1 (3 ions in cavity) in lipid bilayer with no restraints for 1 ns (after the salt-bridge distance restraints were released behind thefilter between Glu138 and Arg148) with 2 fs timesteps (4-core job): afterbridge4 (BioSimGrid_GB-OXF_4696)
Kir2.1 (3 ions in cavity) in lipid bilayer with no restraints for 1 ns (after the salt-bridge distance restraints were released behind the filter between Glu138 and Arg148) with 2 fs timesteps (4-core job with 8 cores allocated): afterbridge (BioSimGrid_GB-OXF_4697)
Kir2.1 in lipid bilayer; production run: prod0 (BioSimGrid_GB-OXF_4715)
Kir2.1 in lipid bilayer; production run: prod1 (BioSimGrid_GB-OXF_4735)
Kir2.1 (closed-state chimera-templated) in lipid bilayer; production run after restrained equilibration (no ion in cavity initially): prod0 (BioSimGrid_GB-OXF_4875)
Kir2.1 (closed-state chimera-templated) in lipid bilayer; production run after unrestrained equilibrationprod1 (BioSimGrid_GB-OXF_4915)
Kir2.1 (closed-state chimera-templated) in lipid bilayer; production run after restrained equilibration (no ion in cavity initially): prod1 (BioSimGrid_GB-OXF_4935)
Kir2.1 (closed-state chimera-templated) in lipid bilayer; production run after restrained equilibration (with ion in cavity initially): prod1 (BioSimGrid_GB-OXF_4955)
Kir2.1 (closed-state chimera-templated) in lipid bilayer; production run after restrained equilibration (no ion in cavity initially): prod2 (BioSimGrid_GB-OXF_4997) new!
Kir2.1 (closed-state chimera-templated) in lipid bilayer; production run after restrained equilibration (with ion in cavity initially): prod2 (BioSimGrid_GB-OXF_5015) new!
Kir2.1 (closed-state chimera-templated) in lipid bilayer; production run after restrained equilibration (with ion in cavity initially): KDB S302 'cavity'; downsampled from BioSimGrid_GB-OXF_4895, BioSimGrid_GB-OXF_4955, and BioSimGrid_GB-OXF_5015 (BioSimGrid_GB-OXF_5039) new!
Kir2.1 (closed-state chimera-templated) in lipid bilayer; production run after restrained equilibration (with 7 ions in cavity initially): 'crowd' prod0 (10 ns to 20 ns; previous: BioSimGrid_GB-OXF_5095) (BioSimGrid_GB-OXF_5115) new!
Kir2.1 (closed-state chimera-templated) in lipid bilayer; production run after restrained equilibration (with 3 ions in cavity initially): 'threeion' prod0 (0 ns to 10 ns) (BioSimGrid_GB-OXF_5136) new!
Kir2.1 (closed-state chimera-templated) in lipid bilayer; production run after restrained equilibration (with 3 ions in cavity initially): 'threeion' prod0 (10 ns to 20 ns; previous: BioSimGrid_GB-OXF_5136) (BioSimGrid_GB-OXF_5155) new!

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