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Aug 24, 2020, 11:06:05 AM8/24/20

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These commands which i have used sequentially...but command no. 4 not completed yet after 10 days...how much it will take to complete.

are all commands OK and also their sequence of running one after another.?..

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

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