Please help me understand my issue here. I have run two simulations in series,
the first for 5ns and the second for 5 ns. The second 5ns simulation is merely a
continuation of the first. My prod.in file for the production simulation is as
follows:
&cntrl
imin=0,irest=1,ntx=5,
nstlim=2500000,dt=0.002,
ntc=2,ntf=2,
cut=8.0, ntb=2, ntp=1, taup=2.0,
ntpr=500, ntwx=500,
ntt=3, gamma_ln=2.0,
temp0=300.0,
/
thus, I am generatring a frame per ps, correct? If so, the 2 simulations must
comprise 10,000 frames- is this assumption correct?
I am interested in reading frames 6,000-8,000 into mmpbsa.py and thus obtain
binding data. I have the submit file for mmpbsa.py as follows:
mpirun -np 4 /gpfs1/apps/chemistry/amber/amber11/bin/MMPBSA.py -O -i
mmpbsa_g1tetra.in -o G1TETRA_RESULTS_MMPBSA.dat -sp g1tetra.top -cp
g1tetra_nosolv.top -rp g1tetra_dimer1_no
solv.top -lp g1tetra_dimer2_nosolv.top -y g1tetra_prod_mdx*
My thinking is that the program will read in both trajectories and choose frames
6,000-8,000 and process them. However, this does not work as I get the following
error message:
FYI ptrajSetupIO(): trajin stop value (8000) is greater than the number of sets
read in.
Setting stop to the maximum value (5000)
WARNING in ptrajSetupIO(): trajectory start is > stop; no
configurations will be processed
Thus, only 5,000 frames are read. However- 10,000 should be present.
Can anyone help me with this?
Thanks
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Received on Wed Mar 23 2011 - 10:00:03 PDT
