g_mmpbsa keeps running and does not finish even after 4 days.

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SM

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Sep 5, 2019, 6:29:05 AM9/5/19
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Request for your help in running g_mmbpsa command.

I have given the following command for my protein (particularly NBD domain-384 residues) and an inhibitor as the ligand.
Command:g_mmpbsa -f trajfinal.xtc -s md_0_1.tpr -i pbsa.mdp -pbsa -mm energy_MM.xvg -pol polar.xvg -apol apolar.xvg -b 55000 -e 100000 -dt 10 -n index.ndx.

It has been four days already but the simulation has not stopped , It seems to be going In a loop motion even though the output files for this command have been generated. I tried troubleshooting but I'm unable to reach a conclusion. The screenshot during run is as follows:

Parsing input file p1bH3XoA.in...
Vio_ctor2: Gethostbyname fail INET sock <> dueto <ENOENT>
NOsh:  Deprecated use of ION keyword! Use key-value pairs
NOsh:  Deprecated use of ION keyword! Use key-value pairs
NOsh:  Deprecated use of ION keyword! Use key-value pairs
NOsh:  Deprecated use of ION keyword! Use key-value pairs
Parsed input file.
Got paths for 1 molecules
Reading PQR-format atom data from p1bH3XoA.pqr.
Vio_ctor2: Gethostbyname fail INET sock <> dueto <ENOENT>
  3808 atoms
  Centered at (4.141e+01, 3.523e+01, -1.536e+01)
  Net charge -4.00e+00 e
Preparing to run 4 PBE calculations.
----------------------------------------
CALCULATION #1 (mol1): MULTIGRID
  Setting up problem...
  Vpbe_ctor:  Using max ion radius (1.81 A) for exclusion function
  Debye length:  7.95385 A
  Current memory usage:  506.917 MB total, 3170.576 MB high water
  Grid dimensions: 129 x 129 x 129
  Grid spacings: 1.181 x 1.049 x 1.758
  Grid lengths: 151.196 x 134.272 x 225.003
  Grid center: (62.651, 51.820, 28.170)
  Multigrid levels: 6
  Molecule ID: 1
  Linearized traditional PBE
  Multiple Debye-Huckel sphere boundary conditions
  2 ion species (0.150 M ionic strength):
    0.950 A-radius, 1.000 e-charge, 0.150 M concentration
    1.810 A-radius, -1.000 e-charge, 0.150 M concentration
  Solute dielectric: 2.000
  Solvent dielectric: 80.000
  Using "molecular" surface definition;harmonic average smoothing
  Solvent probe radius: 1.400 A
  Temperature:  300.000 K
  Electrostatic energies will be calculated
  Solving PDE (see io.mc* for details)...
  Calculating energy (see io.mc* for details)...
  Total electrostatic energy = 1.311467158546E+04 kJ/mol
  Calculating forces...
----------------------------------------
CALCULATION #2 (mol1): MULTIGRID
  Setting up problem...
  Vpbe_ctor:  Using max ion radius (1.81 A) for exclusion function
  Debye length:  7.95385 A
  Current memory usage:  506.917 MB total, 3170.576 MB high water
  Grid dimensions: 129 x 129 x 129
  Grid spacings: 0.497 x 0.477 x 0.527
  Grid lengths: 63.630 x 61.020 x 67.441
  Grid center: (41.568, 35.073, -15.610)
  Multigrid levels: 6
  Molecule ID: 1
  Linearized traditional PBE
  Boundary conditions from focusing
  2 ion species (0.150 M ionic strength):
    0.950 A-radius, 1.000 e-charge, 0.150 M concentration
    1.810 A-radius, -1.000 e-charge, 0.150 M concentration
  Solute dielectric: 2.000
  Solvent dielectric: 80.000
  Using "molecular" surface definition;harmonic average smoothing
  Solvent probe radius: 1.400 A
  Temperature:  300.000 K
  Electrostatic energies will be calculated
  Solving PDE (see io.mc* for details)...
  Calculating energy (see io.mc* for details)...
  Total electrostatic energy = 1.387168343604E+05 kJ/mol
  Calculating forces...
----------------------------------------
CALCULATION #3 (mol2): MULTIGRID
  Setting up problem...
  Vpbe_ctor:  Using max ion radius (1.81 A) for exclusion function
  Debye length:  0.889267 A
  Current memory usage:  506.917 MB total, 3170.576 MB high water
  Grid dimensions: 129 x 129 x 129
  Grid spacings: 1.181 x 1.049 x 1.758
  Grid lengths: 151.196 x 134.272 x 225.003
  Grid center: (62.651, 51.820, 28.170)
  Multigrid levels: 6
  Molecule ID: 1
  Linearized traditional PBE
  Multiple Debye-Huckel sphere boundary conditions
  2 ion species (0.150 M ionic strength):
    0.950 A-radius, 1.000 e-charge, 0.150 M concentration
    1.810 A-radius, -1.000 e-charge, 0.150 M concentration
  Solute dielectric: 2.000
  Solvent dielectric: 1.000
  Using "molecular" surface definition;harmonic average smoothing
  Solvent probe radius: 1.400 A
  Temperature:  300.000 K
  Electrostatic energies will be calculated
  Solving PDE (see io.mc* for details)...
  Calculating energy (see io.mc* for details)...
  Total electrostatic energy = 2.708012514367E+04 kJ/mol
  Calculating forces...
----------------------------------------
CALCULATION #4 (mol2): MULTIGRID
  Setting up problem...
  Vpbe_ctor:  Using max ion radius (1.81 A) for exclusion function
  Debye length:  0.889267 A
  Current memory usage:  506.917 MB total, 3170.576 MB high water
  Grid dimensions: 129 x 129 x 129
  Grid spacings: 0.497 x 0.477 x 0.527
  Grid lengths: 63.630 x 61.020 x 67.441
  Grid center: (41.568, 35.073, -15.610)
  Multigrid levels: 6
  Molecule ID: 1
  Linearized traditional PBE
  Boundary conditions from focusing
  2 ion species (0.150 M ionic strength):
    0.950 A-radius, 1.000 e-charge, 0.150 M concentration
    1.810 A-radius, -1.000 e-charge, 0.150 M concentration
  Solute dielectric: 2.000
  Solvent dielectric: 1.000
  Using "molecular" surface definition;harmonic average smoothing
  Solvent probe radius: 1.400 A
  Temperature:  300.000 K
  Electrostatic energies will be calculated
  Solving PDE (see io.mc* for details)...
  Calculating energy (see io.mc* for details)...
  Total electrostatic energy = 1.535080904662E+05 kJ/mol
  Calculating forces...
----------------------------------------
PRINT STATEMENTS

print energy 1 (mol1) - 2 (mol2) end
  Local net energy (PE 0) = -1.479125610586E+04 kJ/mol
  Global net ELEC energy = -1.479125610586E+04 kJ/mol
----------------------------------------
CLEANING UP AND SHUTTING DOWN...
Destroying force arrays.
No energy arrays to destroy.
Destroying multigrid structures.
Destroying 1 molecules
Final memory usage:  0.001 MB total, 3170.576 MB high water


Thanks for using APBS!



Seketoulie Keretsu

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Sep 5, 2019, 6:42:53 AM9/5/19
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For a desktop with corei5 processors, it takes typically about 1 day to get  energy values from 10,000 ns with dt=50  . Since you're doing it for 45000 ns(100-55) with  dt=10 this will take much more time on a personal computer. Might even go for more than 10 days on a PC unless you have a better system setup. 

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Nikhil Maroli

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Sep 5, 2019, 7:03:25 AM9/5/19
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try for smaller trajectories, instead of whole trajectory

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Nikhil Maroli

SM

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Sep 5, 2019, 8:50:02 AM9/5/19
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Oh! OK. thank you.
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SM

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Sep 5, 2019, 8:50:39 AM9/5/19
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Thanks
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Regards,
Nikhil Maroli

SM

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Sep 5, 2019, 8:52:08 AM9/5/19
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Also, this one in the screenshot: "NOsh:  Deprecated use of ION keyword! Use key-value pairs" wont affect results? If yes, how to go about this?


On Thursday, 5 September 2019 16:12:53 UTC+5:30, Seketoulie Keretsu wrote:
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Rafat Ali

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Aug 24, 2020, 11:06:05 AM8/24/20
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I have run 100 ns of simulation, and mm-PBSA analysis is still running even after 10 days...I have used these commands sequentially, and command no. 4 highlighted in red is taking time...it is continuesly running .....



mMPBSA analysis commands......
  

1. Calculation of potential energy in Vacuum


g_mmpbsa -f md_0_1_noPBC.xtc -s md_0_1.tpr -n index.ndx -pdie 2 -decomp


2. Calculation of polar solvation energy


g_mmpbsa -f md_0_1_noPBC.xtc -s md_0_1.tpr -n index.ndx -i polar.mdp -nomme -pbsa -decomp


3. Calculation of non-polar solvation energy

(a) For SASA-only model:

g_mmpbsa -f md_0_1_noPBC.xtc -s md_0_1.tpr -n index.ndx -i apolar_sasa.mdp -nomme -pbsa -decomp -apol sasa.xvg -apcon sasa_contrib.dat


(b) For SAV-only model:

g_mmpbsa -f md_0_1_noPBC.xtc -s md_0_1.tpr -n index.ndx -i apolar_sav.mdp -nomme -pbsa -decomp -apol sav.xvg -apcon sav_contrib.dat


4.One step calculation


g_mmpbsa -f md_0_1_noPBC.xtc -s md_0_1.tpr -n index.ndx -i pbsa.mdp -pdie 2 -pbsa -decomp



5. Average Binding Energy Calculation


python MmPbSaStat.py -m energy_MM.xvg -p polar.xvg -a apolar.xvg





Avrin Ghanaeian

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Aug 24, 2020, 5:55:30 PM8/24/20
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Hello
If you run g_mmpbsa for 100ns it will take forever even in supercomputers. The best way for running large simulations is that you can extract last 10ns or 5ns of your xtc file using this command 
gmx trjconv -s <file_name>.tpr -f <file_namenoPBC>.xtc -o <file_name_noPBC30-50ns>.xtc -n index.ndx -pbc mol -ur compact -b 30000 -e 50001    
and then run the g_mmpbsa for your new 10 or 5ns xtc file.
Best
Avrin




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