Minimization curve

User discussions
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1

I am trying to minimize energy in my protein, but xmgrace gave me a slightly negative curve. I tried to decrease Emtol to 100 but the effect was almost the same. The simulation is carried out in a water environment. I also can’t do nvt equilibration now because it stops on 0 step.Is it possible that it is caused by hydrophobic character of fab domain of my antibody? I also have files that i got when i finished minimization
I need help, please.

img
img797×688 5.73 KB

minim.mdp (1.0 KB)
em.log (2.7 MB)

2

The curve is fine. If mdrun stopped at step 0, then something failed and you should find an informative error message in the .log file or stderr.

3

Dear Justin Lemkul
Is it in em.log file??, and where I could find stderr errors list
?? I also got this
img2
em (2).log (1.2 MB)