[gmx-users] PR after minimisation and PR of missing residues?

minnale minnale_gnos at rediffmail.com
Sun Oct 5 07:26:52 CEST 2008

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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