[gmx-users] Distance calculation
jalemkul at vt.edu
Tue Nov 27 14:51:19 CET 2018
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.
> On Mon, 26 Nov 2018, 00:48 rose rahmani <rose.rhmn93 at gmail.com wrote:
>> 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?
Justin A. Lemkul, Ph.D.
Office: 301 Fralin Hall
Lab: 303 Engel Hall
Virginia Tech Department of Biochemistry
340 West Campus Dr.
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jalemkul at vt.edu | (540) 231-3129
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