[gmx-users] on Umbrella Sampling

[Acoot Brett]

Dear All,
 
In the on-line tutorial "Umbrella Sampling " byJustin Lemkul in "http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/umbrella/05_pull.html" , there is a command "grompp -f md_pull.mdp -c npt.gro -p topol.top -n index.ndx -t npt.cpt -o pull.tpr". Here is the index.ndx exactly same as following?
 
make_ndx -f npt.gro
(> indicates the make_ndx prompt)
> r 1-27
> name 19 Chain_A
> r 28-54
> name 20 Chain_B
> q

 
Then what is the meaning of "r1-27", what is the meaning of " name 19 Chain_A", and what is the meaning of "q"?
 
Suppose I have a protein-peptide complex A, the protein is of 400 aas,the peptide is 20 aas. Suppose I have another protein-peptide complx B, and the only difference beteen protein complex A and complex B is that in position 3 of peptide of complex A, it is Ala. In the coresponsing position of the peptide of complex B, it is Arg.
 
Can the results of this Umbrella Sampling calculation be accurate enough to show that the binding energy between the protein and peptide in complex A and B is different and cuurently reflects the fact that the difference is caused by the substitution of Ala by Arg?
 
I am looking forward to getting a reply from you.
 
Cheers,
 
Acoot
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