[gmx-users] Distance calculation

[rose rahmani]

Great! Non-hydrogen is generally for all AAs, but i want non-hydrogen atoms
of each AA number 1, 2, 3 to be representative of one adsorption. Moreover,
if 4 non-hydrogen atoms of AA were in <0.5 nm, this should be considered as
one adsorption not 4!  How should i come up with these challenges?
And as i'm not much skilled in programming, is there any useful examples
for implementing python or perl in GROMACS?

Best



On Tue, Nov 27, 2018 at 5:21 PM Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 11/26/18 1:59 PM, rose rahmani wrote:
> > Can i use -dist option?
> > Would you please help me?
>
> The -dist option just prints a list of atoms that satisfy the criterion;
> that's not necessarily useful to you.
>
> Use gmx mindist with appropriate selections to get the time series of
> the minimum distance of relevant non-H atoms and your nanotube. Then
> write a simple script that reports some useful quantity, like the first
> time at which the distance criterion was met or the percentage of time
> the distance was below 0.5 nm. This is trivial with something like
> Python or Perl.
>
> -Justin
>
> > On Mon, 26 Nov 2018, 00:48 rose rahmani <rose.rhmn93 at gmail.com wrote:
> >
> >> Hi,
> >>
> >> My system contains 20 amino acids around nanotube. I want to know the
> >> adsorption amount of AA during simulation time; the adsorption occurs
> >> when the distance between one of non-hydrogen atoms of AA and the tube
> >> surface was less than 0.5 nm. So how can i calculate this property?
> >>
> >> Would you please help me?
> >> Best
> >>
>
> --
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> Justin A. Lemkul, Ph.D.
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