[gmx-users] question about polar.mdp file in 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 [1] OBTAINED FROM 
HTTPS://RASHMIKUMARI.GITHUB.IO/G_MMPBSA/HOW-TO-RUN.HTML.  

 I THINK THERE IS SOME PROBLEM, BECAUSE AFTER RUN 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, THE ANALYSIS MAY BE PERFORMED FASTER ?


Best Regards 

   

Links:
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[1]
https://github.com/RashmiKumari/g_mmpbsa/blob/master/test/sasa_orig/mmpbsa.mdp