[gmx-users] g_sgangle problem

Justin Lemkul jalemkul at vt.edu
Sat Jul 28 14:56:53 CEST 2012

On 7/28/12 5:28 AM, yousef nademi wrote:
> hi gromacs users and especially Dr. Justine
> in using the g_sgangle i have to define index file contain multiple of two defining all the P and N atoms but after executing the g_sgangle i get the message:something wrong with contents of index file
> after defining the one p atom and 1 n atom then there was no problem
> should i define all the index file to 2 group part and then average from the rezult
> or should i do something in index file that can solve the problem

In principle, your index group should contain all (P,N) pairs such that the 
overall group size is a multiple of two.  I believe the index group has to be in 
a particular order, like P N P N etc, not all P atoms then all N atoms.

A workaround (though tedious) is to have each (P,N) pair in its own group and do 
the analysis.  You can then obtain averages or distributions of values.  In 
principle though, this should not be necessary.



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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