Hi friends!
I am running my simulations in negative ion mode, gromacs.
The problem is that, my proteins completely unfold, and rotate badly.
At the very begininng they start unfolding and rotationg, I do the energy minimization, equilibration and annealing, but it didn't help!
Can you please advise me?
Thank you
I think in your case since you did not mention it, may have caused the protein to completely unfold and rotate uncontrollable
1) Minimization where the (heavy) atoms of macromolecule are fixed at reference structure, and water and ions (or hydrogen atoms of macromolecule) are allowed to move freely;
2) Simulation annealing in NVT ensemble where again the (heavy) atoms of macromolecule are fixed at reference structure, and water and ions (and hydrogen atoms of macromolecule) are allowed to move freely;
3) Then, the harmonic restraints are applied to (heavy) atoms of macromolecule allowing them to vibrate around reference structure positions, and water + ions (and hydrogen atoms of macromolecule) are allowed to move freely. This simulation is performed using NPT ensemble, and the restraints are slowly removed until the (heavy) atoms of macromolecule are also allowed to move freely.
I think in your case, since you did not mention it, the missing of task 3 may have caused the protein to completely unfold.
I hope it helps!
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