[gmx-users] ACCELERATE SIMULATION

[Aman Deep]

HELLO,

I had run simulation for my protein which has 1200 residues it took 10 days
for 10 ns on simple mdrun command. I have a graphic card with the following
configuration:


  VGA compatible controller: Advanc VGA compatible controller: Advanced
Micro Devices, Inc. [AMD/ATI] Bonaire [FirePro W5100] (prog-if 00 [VGA
controller])
Subsystem: Advanced Micro Devices, Inc. [AMD/ATI] Device 030c
Physical Slot: 4
Flags: bus master, fast devsel, latency 0, IRQ 68
Memory at e0000000 (64-bit, prefetchable) [size=256M]
Memory at f0000000 (64-bit, prefetchable) [size=8M]
I/O ports at e000 [size=256]
Memory at fbe00000 (32-bit, non-prefetchable) [size=256K]
Expansion ROM at fbe40000 [disabled] [size=128K]
Capabilities: <access denied>
Kernel driver in use: radeon
Kernel modules: radeon
ed Micro Devices, Inc. [AMD/ATI] Bonaire      [FirePro W5100] (prog-if 00
[VGA controller])
Subsystem: Advanced Micro Devices, Inc. [AMD/ATI] Device 030c
Physical Slot: 4
Flags: bus master, fast devsel, latency 0, IRQ 68
Memory at e0000000 (64-bit, prefetchable) [size=256M]
Memory at f0000000 (64-bit, prefetchable) [size=8M]
I/O ports at e000 [size=256]
Memory at fbe00000 (32-bit, non-prefetchable) [size=256K]
Expansion ROM at fbe40000 [disabled] [size=128K]
Capabilities: <access denied>
Kernel driver in use: radeon
Kernel modules: radeon

can somebody please tell me command in MDRUN or how to use GPU to
accelerate the simulation?

thank you

-- 
Aman Deep
MSc Bioinformatics
Jamia Millia Islamia
New Delhi - 110025