[gmx-users] Calculation of polar energy question

Justin Lemkul jalemkul at vt.edu
Tue Dec 15 20:56:35 CET 2015

On 12/15/15 2:53 PM, Mishelle Oña wrote:
> 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.
> Please, I need your help

Perhaps you should try contacting the author or posting to the g_mmpbsa help 
forum (https://groups.google.com/forum/#!forum/g_mmpbsa) rather than continually 
post here.  If you're not getting replies, it's because no one knows the answer.



Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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