Is there any methodology to increase the no of cores (for faster computations) being used in the command line for mmpbsa claculations:
g_mmpbsa -f md_0_1.xtc -s md_0_1.tpr -n index.ndx -i pbsa.mdp -pdie 2 -pbsa -decomp
python MmPbSaStat.py -m energy_MM.xvg -p polar.xvg -a apolar.xvg
python MmPbSaDecomp.py -bs -nbs 2000 -m contrib_MM.dat -p contrib_pol.dat -a contrib_apol.dat
The system is taking too long (much more than expected time) to complete a calculation?
Hi Safa Aouinti Anwesh Pandey while calculating python MmPbSaStat.py -m energy_MM.xvg -p polar.xvg -a apolar.xvg
every time i get an error how to resolve it and why it happens ?
Traceback (most recent call last):
File "MmPbSaStat.py", line 332, in
main()
File "MmPbSaStat.py", line 68, in main
cTmp.CalcEnergy(args,frame_wise,0)
File "MmPbSaStat.py", line 87, in CalcEnergy
polEn = ReadData(self.PolFile,n=4)
File "MmPbSaStat.py", line 261, in ReadData
for line in infile:
File "/public/home/xzdu/lib/python3.5/codecs.py", line 321, in decode
(result, consumed) = self._buffer_decode(data, self.errors, final)
UnicodeDecodeError: 'utf-8' codec can't decode byte 0xb8 in position 227: invalid start byte
hi Anwesh Pandey when i calculate average binding energy in result of this electrostatic and binding energy came positive . what would be the reason of that ?
I have used pdie 2 and i also had used pdie 8 but still these energies are positive. how to deal with it ?
Ayesha Kanwal
See, these disscussions could be of some help:
https://www.researchgate.net/post/How_to_deal_with_the_positive_binding_energies_calculated_using_g_mmpbsa_tool
https://www.researchgate.net/post/How_do_I_tackle_positive_binding_energy_in_simulation
Anwesh Pandey i am using g_mmpbsa and i have calculated 100ns md simulation with gromacs and i am using 50 frames from them. to calculate binding free energy.
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