Hi all,
I have two doubts on PR, may be these are trivial to you.
1.According to Gromacs procedure(from Gromacs tutorial) the sequential steps
are (a)Energy minimisation (b)Position restrain with force constant descendant
manner and finally (c)production. Here my doubt that, is it require to do
energy minimisation between PR and production? because after PR the system
equilibrating properly if do one minimisation the structure looses bad contacts
with low energy, am I right?
2.If my desire protein contain some missing residues(from PDB)rectified those
residues by using INSIGHT-II. Later start simulations particularly at PR, is it
require to keep restrain specifically on added missing residues or whole
protein residues in .itp file?
Any suggestions would be appreciated
Thanks in advance.
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