[gmx-users] Distance calculation

Justin Lemkul 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:
>> 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


Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129


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