While attaching topology file it is asking for approval from amber site. I
am resending the same mail again.
Sorry for duplication if any.
To remove the extra point issue I made the topology using TIP3P instead of
TIP4PEW. I tried a test run using pmemd.cuda on individual machines and its
running fine without any error. I checked that with cpu serial and multiple
processors there are no errors and are running fine there as well.
One question as said earlier that amber 12 does not really gain much using
multiple GPUs. Is it the problem with AMBER 12 or AMBER 11 as well.
Technical specifications for my computers are
*CPU/Processor *
2x 8-core Intel Xeon® E5-2670 with 20MB Cache . 2.6Ghz
*RAM *
64GB ECC DDR 3,1600MHz equal distribution of memory on DIMMs
*GPU *
NVIDIA K20
*CPU:GPU Ratio*
2:2 only on Compute nodes with GPU Cards
*GPU Memory*
6GB per GPU
*Connectivitybetween CPU andGPU*
Dedicated 16xPCI Express bus (Gen 3.0)
Input files are with the attachment for the test run
Heating the system with 25 kcal/mol restraints on protein,at constant volume
&cntrl
imin = 0, ntx=1, ntb=2, ntp = 1, taup=2.0, cut = 10,
ntc = 2, ntf = 2, tempi = 0.0, temp0 = 300.0, ntt = 3,
gamma_ln = 1.0, nstlim = 500, dt = 0.002, ntpr =50, ntwx = 50, ntwr = 50
/
for checking purposes, I have removed the restraints for now.
Topology and coordinate files are with the attachment.
Thanks
Ashutosh
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Received on Wed Nov 20 2013 - 09:30:03 PST
