AMBER Archive (2008)
Subject: Re: AMBER: pmemd
From: Robert Duke (rduke_at_email.unc.edu)
Well, at a minimum we would need the mdin input and info about the system (reflected in the prmtop/inpcrd) to even begin guessing. PMEMD does a lot of what sander does, but not everything (the differences are detailed in the manual). Also, presuming the executable for pmemd is good and the lam installation is good, you should have at least gotten some output in run11.out, or in your stderr file, wherever that is going. How many cpu's are you attempting to use? How many did you use for sander.MPI?
I am simulating a protein in explicit water, and I've been using sander with lamwrapper, but want to use pmemd, as I understand it is faster. However, I've been having trouble running the jobs. I'm not sure where to start with this, so any help would be appreciated.
My submission script is:
#PBS -N run11
The output file is:
PBS assigned these nodes:
First task running on:
LAM 7.1.1/MPI 2 C++/ROMIO - Indiana University
No dedicated nodes so no cleanup done.
Thanks in advance,