[gmx-users] calculation of polar solvation energy using MMPBSA

[mmousivand93]

Dear  all 

 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
https://rashmikumari.github.io/g_mmpbsa/how-to-run.html [1].  

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 [2]] 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? 

Best 

Links:
------
[1] https://rashmikumari.github.io/G_MMPBSA/HOW-TO-RUN.HTML
[2]
https://github.com/RashmiKumari/g_mmpbsa/blob/master/test/sasa_orig/mmpbsa.mdp