Jason,
Thanks for the explanation. There's a second point that I'd like to clarify - if possible.
My 10ns trajectory is made up of 5 individual trajectories of 2ns and 200 frames each.
If I use an input file such as the one below
&general
endframe=50, keep_files=2,
/
&nmode
nmstartframe=5, nmendframe=45,
nminterval=5, nmode_igb=1, nmode_istrng=0.1,
/
I get
Calculations performed using 250 frames.
|NMODE calculations performed using 9 frames.
Setting the endframe=200 and
nmstartframe=5, nmendframe=200,
nminterval=10
I get "Master thread is calculating normal modes for 5 frames".
It's a bit esoteric for me the way the program works out the number of frames. Any explanation would be most welcome.
Regards
George
On Oct 3, 2011, at 9:47 PM, Jason Swails wrote:
> On Mon, Oct 3, 2011 at 2:01 PM, George Tzotzos <gtzotzos.me.com> wrote:
>
>> I'm running MMPBSA.MPI on 12 processors. I'm trying to compute the entropy
>> (nmode) of a protein/ligand complex from a 10ns trajectory (1000) frames.
>>
>> My entropy.in is:
>>
>> Input file for running entropy calculations using NMode
>> &general
>> endframe=1000, keep_files=2,
>> /
>> &nmode
>> nmstartframe=10, nmendframe=990,
>> nminterval=10, nmode_igb=1, nmode_istrng=0.1,
>> /
>>
>>
>> My estimate is that it'll take at least 10 hours to get results.
>>
>
> Normal mode estimates are fairly unreliable. As expensive as the Hessian
> construction/diagonalization is (we're helped by the fact that it's an
> analytical Hessian, I think), in my experience the minimization takes
> significantly longer. However, the number of steps required to minimize
> within tolerable limits obviously depends on how close the structure is to a
> minimum initially. MMPBSA.MPI's parallelization scheme is naive, though,
> and assumes each will take the same amount of time, which hurts parallel
> scaling for normal mode calcs in most cases.
>
>
>>
>> My question is whether increasing nminterval to 100 would compensate the
>> accuracy of the calculation.
>>
>
> Unlikely (though maybe increase it to 50 instead). Keep in mind that NMODE
> frames are minimized, so in all likelihood many of your snapshots are very
> structurally similar to others (if they reduce to the same local minimum).
> A better approach may be to perform normal mode analysis on clustered
> trajectories, and only take one snapshot from each cluster (or something
> like that). You can always check existing literature to see what they've
> done as well.
>
> HTH,
> Jason
>
>
>> Thanks in advance
>>
>> George
>>
>>
>>
>>
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>
>
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Candidate
> 352-392-4032
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Received on Tue Oct 04 2011 - 07:00:02 PDT
