Hi all,
I am using Amber11 and AmberTools 1.5. 10 ns simulations of an inhibtor with protein A and B have been conducted respectively. There are about 350 AA in each complex. The common input file of complex A and B is as following:
Input file for running entropy calculations using NMode
&general
startframe=3500, endframe=5000, keep_files=2, interval=10,
/
&nmode
nmstartframe=1,
nminterval=10, nmode_igb=1, nmode_istrng=0.1,
/
Here is the comand line:
mpirun -np 12 MMPBSA.MPI -O -i mmpbsa.in -o MMPBSA.dat -sp com_sol.prmtop -cp com_solv.prmtop -rp receptor.prmtop -lp ligand.prmtop -y ../com.mdcrd
It takes about 3 days to finish the NMode entropy calculation of 15 frames of complex A's trajectory.
The problem is, in complex B's case, the CPU numebers reduced from 12 to 8 abnormally and it has been 7 days till now. While the job is still running. Should I wait or kill the task? Why did this phenomenon happen?
Many thanks.
Cao Yang,
Zhejiang University.
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Received on Mon Jun 11 2012 - 21:30:03 PDT
