[gmx-users] energy minimization

farial tavakoli farial.tavakoli at ymail.com
Tue Feb 20 10:52:46 CET 2018

Dear GMX users
I used CHARMM36 all atom force field to generate .top and .gro files for my complex composed of a receptor protein and a ligand with 2 phosphotyrosine residues, then ran a md simulation on it and then used g_mmpbsa to calculate the binding free energy by pdies ( 2 and 4) but got + 426 and +527 kjol/mol, respectively. While, I calculated binding energy before for many other complexes without any phosphate groups using OPLS all atom force field and pdie = 2 and obtained minus energy. But this time , I dont know why I got positive binding energy? Is it because of charmm36 all atom force field , the phosphate groups or it is needed to be energy minimized under more restriction situations? 
I am checking different factors to understand its reason, so I wanted to know , would it be ok if I energy minimize the complex with more restriction situations ? for example by specifying emtol under 1000 kj/mol/nm , like 800 ? I think the positive binding energy might be because of the complex didnt minimized well. however I checked the em.log file and saw it was minimized well:

Steepest Descents converged to Fmax < 1000 in 241 steps
Potential Energy  = -6.5047744e+05
Maximum force     =  9.8285083e+02 on atom 3335
Norm of force     =  3.6905827e+01
Is there anyone can advice me in energy minimization with emtol 800? 
Thank in advanceFarial

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