According to your input file, prod.in, you are running 2500000 steps, and
writing to the trajectory every 500 steps (ntwx=500), this means that the
trajectory file should have 2500000/500 = 5000 total frames. You would neat
to write to the trajectory file every 250 steps if you want 10,000 frames in
the trajectory.
I hope that helps.
-Bill
On Wed, Mar 23, 2011 at 12:44 PM, Chris Chris <alpharecept.yahoo.com> wrote:
> 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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>
--
Bill Miller III
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-6715
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Received on Wed Mar 23 2011 - 10:00:04 PDT
