NMODE Entropy Calculations Error

[Vijay Sai Cheerala]

Dear Sir,

I am getting an error when I am running NMODE Entropy calculations.

...............................................................................................................................

The error is:

File "/home/research/miniconda3/envs/gmxMMPBSA/bin/gmx_MMPBSA", line 8, in <module>
    sys.exit(gmxmmpbsa())
  File "/home/research/miniconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/app.py", line 103, in gmxmmpbsa
    app.file_setup()
  File "/home/research/miniconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/main.py", line 138, in file_setup
    lig_frames, self.numframes_nmode) = make_trajectories(INPUT, FILES, self.mpi_size,
  File "/home/research/miniconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/make_trajs.py", line 222, in make_trajectories
    nmtraj.Setup(INPUT['nmstartframe'], INPUT['nmendframe'], INPUT['nminterval'])
  File "/home/research/miniconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/make_trajs.py", line 509, in Setup
    raise TrajError('start frame (%d) > total frames (%d)' %
TrajError: start frame (4300) > total frames (101)
Exiting. All files have been retained.

The input is:

&general
sys_name="NMode",
startframe=4000,
endframe=5000,
interval=10
forcefields="leaprc.protein.ff14SB",
PBRadii=2,
/
&gb
igb=1, saltcon=0.150,
/
&nmode
nmstartframe=4300,
nmendframe=5000,
nminterval=100,
maxcyc=50000, drms=0.001,
/

..............................................................................................................................

Please help me.

Thanks & Regards

Vijay Sai

[Mario Sergio Valdes]

As clarified in the documentation footnote " Thus, the "trajectory" from which the snapshots will be chosen for the nmode calculations will be the set of snapshots on which the other calculations were performed", you must define nmstartframe in the frame of the selected set of frames. That is, in your case, to calculate only 7 frames, you must define it as nmstartframe = 30, nminterval = 10.

Schema:

1    100    1000   2000    3000   4000                                                5000

|-------|---------|----------|-----------|----------|--------------------------------------------------|           Energy

                                                         |--------------------------------------------------|           NMODE

                                                         1                                                      101

HTH!

Mario S.