[gmx-users] on Umbrella Sampling

[Justin A. Lemkul]

Acoot Brett wrote:
> Here I also mean how can I get the index.npt in the "grompp -f 
> md_pull.mdp -c npt.gro -p topol.top -n index.ndx -t npt.cpt -o pull.tpr".
>  
> Looking forward to getting your advice.
>  

That file is produced by make_ndx.  It is written when you type 'q' and Enter to 
quit the program.  If you have not specified any other output name, the default 
is "index.ndx."

-Justin

> Cheers,
>  
> Acoot
> 
> *From:* Justin A. Lemkul <jalemkul at vt.edu>
> *To:* Acoot Brett <acootbrett at yahoo.com>; Discussion list for GROMACS 
> users <gmx-users at gromacs.org>
> *Sent:* Sunday, 1 April 2012 10:32 PM
> *Subject:* Re: [gmx-users] on Umbrella Sampling
> 
> 
> 
> 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?
>  > 
> 
> Probably.
> 
> -Justin
> 
> -- ========================================
> 
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> 
> ========================================
> 
> 

-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================