Sorry, I made a mistake in reading your e-mail. You are right, you should
have 10,000 total frames by running the two back-to-back simulations. Have
you tried reading these trajectories into ptraj to make sure they each have
10,000 total frames?
-Bill
On Wed, Mar 23, 2011 at 12:52 PM, Bill Miller III <brmilleriii.gmail.com>wrote:
> 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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>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
>
> --
> Bill Miller III
> Quantum Theory Project,
> University of Florida
> Ph.D. Graduate Student
> 352-392-6715
>
--
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 - 10:00:05 PDT
