[gmx-users] on Umbrella Sampling

Justin A. Lemkul jalemkul at vt.edu
Sun Apr 1 14:32:36 CEST 2012

Acoot Brett wrote:
> Dear All,
> In the on-line tutorial "Umbrella Sampling " by*Justin 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"?

Type "help" at the make_ndx prompt for an explanation.

> 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?




Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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