We recently obtained our Amber18 license and while testing the new installation I ran into a few problems. Well, just one, really.
First of all, my system configuration:
Cuda compilation tools, release 9.0, V9.0.176
Driver Version: 384.81
Centos 6.4
gcc (GCC) 4.4.7 20120313 (Red Hat 4.4.7-23)
Amber18/Ambertool18 up-to date
When running a normal simulation, the temperature equilibration step has some weird increases in potential and total energy. These raises result in a
distorted protein structure. Both energies return to "normal" (as compared to an identical simulation in Amber 16) during the pressure equilibration.
Previous steeps, energy minimization with position restraints, seem normal. I have ran the same simulation in the same hardware and same compilers using CUDA but with Amber16 but no energy raise and with "normal" protein structures.
Here is my input for equilibration, in dropbox: https://www.dropbox.com/s/tw7jer7zz8pfo54/md1.in?dl=0
Can somebody see any mistake I made and cannot identify myself?
Thank you and best regards.
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Received on Sun Nov 18 2018 - 20:00:02 PST
