[gmx-users] Getting started / tutorial speptide example g_energy and xmgrace

[Dr. Daniel James White PhD]

Hi All,

We are trying to run through the speptide examples in the gromacs  
tutorials
as described in
http://www.gromacs.org/documentation/reference3.1/online/ 
getting_started.html#start

everything is fine except for 2 things

1) we get 850 waters instead of 2500 as it says in the webpage
2) when trying to find out if , I quote
"A good check of your silulation is to see whether density and  
potential energies have converged:"
using  the g_energy prog.
ok, the prog starts and you are given a list of different energies it  
can calculate,
so we type
9 0
and get the potential energy, great.
but how do we get the density energy to complare it with, there is no  
option for that in g_energy.

Also xmgrace is not installed on my system (should it have come with  
the gromacs3.1.4-1 rpm package?

where should I get xmgrace from please

cheers

Dan


Dr. Daniel James White BSc. (Hons.) PhD
Cell Biology
Department of biological and environmental science
University of Jyväskylä
Jyväskylä
Finland
+358 (0)14 260 4183 (work)
+358 (0)414740463 (mob)

http://www.chalkie.org.uk
dan at chalkie.org.uk
white at cc.jyu.fi