[gmx-users] on Umbrella Sampling
Justin A. Lemkul
jalemkul at vt.edu
Sun Apr 1 14:49:57 CEST 2012
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
========================================
More information about the gromacs.org_gmx-users
mailing list