[gmx-users] X and Y dimensions in nanometers

Dallas Warren Dallas.Warren at monash.edu
Fri Sep 9 05:30:54 CEST 2011

What was the issue you had with g_gyrate?  As that is the best tool for this job.  Do you have pbc issues?

Catch ya,

Dr. Dallas Warren
Medicinal Chemistry and Drug Action
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3010
dallas.warren at monash.edu
+61 3 9903 9304
When the only tool you own is a hammer, every problem begins to resemble a nail.

From: gmx-users-bounces at gromacs.org [mailto:gmx-users-bounces at gromacs.org] On Behalf Of Conrado Pedebos
Sent: Friday, 9 September 2011 4:13 AM
To: gmx-users at gromacs.org
Subject: [gmx-users] X and Y dimensions in nanometers

Dear gmx-users,

I am working with a system composed by 20 molecules which are aggregated in water. I want to calculate the dimensions of this aggregate, but it has an elipsoidal shape, instead of a globular shape, as follows in this representation:

-----( ____________)------X

Which gromacs tool could I use to perform this analysis and calculate X and Y (nm) as a function of time?

I tried using g_gyrate and observing the Rx, Ry and Rz components, but I couldn't get it right.

Thanks in advance,

Conrado Pedebos.
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