[gmx-users] calculation of polar solvation energy using MMPBSA
mmousivand93 at ut.ac.ir
Thu May 30 12:12:26 CEST 2019
I run molecular simulation for DNA-small molecule complex (50 ns), I
want to analysis using MMPBSA, for polar solvation energy calculation
,I used the mmpbsa.mdp obtained from
After running this command"_g_mmpbsa -f traj.xtc -s topol.tpr -i
mmpbsa.mdp -n index.ndx -nomme -pbsa -decomp -apol apolar.xvg -apcon
contrib_apol.dat_" , the analysis was so slowly,however there are
special item in mmpbsa.mdp [1 ] as fallow:
"maximum memory (in mb) available per-processor for a calculation.
gmemceil = 4000"
if I change the item in mdp file(maximum memory), the analysis may be
performed faster ?
Also,I have another question, is it correct to select receptor as group
1 and ligand as group when we want to calculat polar solvation ?
Is it correct to use the same polar.mdp file for our analysis as you put
in tutorial file?
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