[gmx-users] Gmx distance

Dallas Warren dallas.warren at monash.edu
Sun Oct 28 23:12:14 CET 2018

Couple of methods come to mind:
# cut the box into slices, small enough so that angle between the tube
axis and line to the AA has little effect on the distance.  Then do
COM to AA analysis in each slice, then "add" the slice results
together.  This is an approximation.
# align tube axis along one of the axes, then measure the distance
components, then calculate from the appropriate x,y,z pair of terms.
If correctly align, this will be most accurate.

Catch ya,

Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3052
dallas.warren at monash.edu
When the only tool you own is a hammer, every problem begins to resemble a nail.

On Sat, 27 Oct 2018 at 23:03, rose rahmani <rose.rhmn93 at gmail.com> wrote:
> Hi,
> I want to calculate distances between fixed tube in the middle of the box
> and amino acids(all are same type)around it. But gmx distance gives me the
> relative distance i mean AA can be front or back( can be 0.5 or -0.5 from
> tube) of  tube but still |-0.5|=0.5 nm far from it. How can i have the
> absolute value of distances?
> Would you please help me?
> Best
> Rose
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