Nmode calculations are very computationally demanding and could easily take this long depending on system size and available computer resources. Without knowing these details, though, it is difficult to assess whether this is expected or not for your calculation.
-Bill
On Sep 14, 2012, at 4:54 AM, Dilraj LAMA <dilrajl.bii.a-star.edu.sg> wrote:
> Dear Amber users,
> I am trying to use the python script for MMPBSA
> calculation. As a test, I am running the calculation on two snapshot
> from my trajectory. The PB and GB calculation went of fine but am
> having issues with the NMODE calculation.
>
> It is taking unusually long time to perform the calculation (close to
> 10hours of CPU time)
>
> Here is my input script.
>
> --------------------------------------
> sample input file for NMODE calculation
> &general
> startframe=1, endframe=10, interval=5,
> verbose=1, keep_files=0, strip_mdcrd=0,
> /
> &nmode
> dielc=1.0,
> nmstartframe=1, nmendframe=2, nminterval=1,
> maxcyc=10000, drms=0.001,
> nmode_igb=1, nmode_istrng=0.1,
> /
> --------------------------------------
> I am using the serial version of MMPBSA.py.
>
> Its just a two frame calculation, So shouldn't take that long.
>
> Am I missing something? Will be glad if someone give me an insight.
>
> Thank you,
> Dilraj.
>
>
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Received on Fri Sep 14 2012 - 04:30:02 PDT
