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

Justin A. Lemkul jalemkul at vt.edu
Sun Oct 5 16:10:06 CEST 2008

minnale wrote:
> 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? 

There is no need to run EM after PR.  EM simply gives the system a reasonable 
starting point, energetically speaking.

> 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?     

I don't see any reason not to restrain the entire protein, as long as it is intact.


> Any suggestions would be appreciated
> Thanks in advance.
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Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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