That will still allow peptide atoms to move (if only a little).
AFAIK Gromacs is not really fit for rigid body studies, but you can set
all bonds and angles to constraints (mdp option:
constraints=all-angles). This may or may not work. Torsion angles will
still be free to rotate though. From the
When you run EM with -v directive, you will see how much is the largest
force value applies to your atom. Try to estimate whether that force
constant was enough to keep your atom fix because if your structure has any
overlap, force can be very large
On Thu, Feb 7, 2019 at 6:40 AM Ashraya
Hi,
I am trying to do position restrained energy minimization of a solvated
peptide, where the peptide is restrained but the solvent is free to move.
But I do see the positions of the atoms of the peptide change. I increased
the force value in position restraint file to 1 from 1000, but it
Hi,
I am trying to do position restrained energy minimization of a solvated
peptide, where the peptide is restrained but the solvent is free to move.
But I do see the positions of the atoms of the peptide change. I increased
the force value in position restraint file to 1 from 1000, but it
