[gmx-users] energy minimization

[Justin Lemkul]

On 2/20/18 4:52 AM, farial tavakoli wrote:
> 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?

The purpose of energy minimization is to establish a reasonable starting 
point for your simulation. Tweaks to emtol will have little to no 
noticeable bearing on the conformational ensemble generated by MD.

-Justin

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Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

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jalemkul at vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

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