[gmx-users] Problems with g_mmpbsa
samimishu at hotmail.com
Mon Dec 14 21:41:10 CET 2015
Hi, I am using g_mmpbsa tool for calculate the solvation energy of molecule. From the paper Kumari et al (2014) g_mmpbsa - A GROMACS tool for high-throughput MM-PBSA calculations. J. Chem. Inf. Model.54:1951-1962. I understand that solvation energy is the sum of polar and nonpolar energies so I start calculating the polar component with this command: g_mmpbsa -f sinagua.trr -s topol.tpr -i mmpbsa.mdp -n index.ndx -nomme -pbsa -pol polar.xvg -nodiff It started to appear something like calculation 1- calcultation 2-calcultation 3- calcultation 4 and it repeats over and over again.
I don´t have much experience with this tool. Could you tell me how long it takes to do an average calculation with this tool?. Also I want to know if it is normal that the tool repeats calculation 1- calcultation 2-calcultation 3- calcultation 4 over and over again.
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