[gmx-users] on Umbrella Sampling
Justin A. Lemkul
jalemkul at vt.edu
Sun Apr 1 14:44:22 CEST 2012
Acoot Brett wrote:
> I have type the help at the prompt of make_ndx, but it does not give the
> explaination as I expected. Thus I hope you can give me an explaination
> based on your tutorial.
What were you expecting that you didn't get? The help information describes all
of the sytax. For instance, it contains the following lines:
'name' nr name : rename group nr to name.
'r' nr1 - nr2 : selects residues in the range from nr1 to nr2.
'q' : save and quit.
Those lines alone directly answer your questions.
> *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
> , 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
> > 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
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
Justin A. Lemkul
ICTAS Doctoral Scholar
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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