Dear sir
wish you are fine !
I was trying to apply AMBER Advanced Tutorial 22 of the Accelerated
molecular dynamics on my target protein to detect some conformational
change. I did all the following preparation steps "with some minor changes
in the supported control files to suite my protein" successfully
Minimize only the water, restraining the protein (20000 cycles)
Let water move (NTP, 300K), restraining the protein
Minimize water and protein (20000 cycles)
Heat the system, restraining the protein (NVT 0 to 300K)
Relax the system, restraining the protein heavy atoms (NPT, 300K,
0.5ns)
Relaxthe system (NPT, 300K, 5ns)
However once I calculated the AMD parameters EthreshP, alphaP, EthreshD &
alphaD as described in the manual and tried to run the last step of the
production AMD, I faced an error of " vlimit exceeded " at the first 1000
steps. I've decreased the time step from 0.002 to 0.001 ps and run again
.this just postponed the error after the first 1000 steps to 1020 md steps.
Any suggestions ?!!!
Best Regards
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Sun Feb 01 2015 - 03:00:03 PST
