Sasha:
a couple of things
how big is your system? number of atoms, box size ?
Second, and as a general idea. NEVER change two things at once, you would never know where problems came from. When going from Amber 10 to 11 and now to 12, you did not just changed the amber version but also went from cpu to gnu.
Try running on amber12 on cpu first. We can then try to isolate your problems.
Adrian
________________________________________
From: Sasha Perkins [slperks49.gmail.com]
Sent: Saturday, November 10, 2012 10:32 AM
To: AMBER Mailing List
Subject: Re: [AMBER] System blows up after several nanoseconds using Amber 12
Jason,
Thanks for the prompt reply. I agree with you that the cut off is very
large. The only reason I'm using that cut off is because in the literature,
that is the typical cut off for my type of system and so I tried that
first.
The latest bugfix for Amber12 we have is 26.
I am using the Penn State Lion-GA cluster with only one GPU for now
using pmemd.cuda_SPFP.MPI. The Lion-GA cluster GPUs I believe are Nvidia
Tesla M2090. Should I be using a different command if I'm only running in
one GPU? Or simply use more GPUs?
Thanks in advance for your help,
Sasha Perkins
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Received on Sat Nov 10 2012 - 08:00:03 PST
