[gmx-users] tutorial speptide

Dr. Daniel James White PhD dan at chalkie.org.uk
Wed May 14 11:24:00 CEST 2003

Hi all,

Newbie questions:

Why does it tell you to check the density using g_energy in the 
speptide tutorial if this information is not generated by the tutorial 

Now I have xmgrace working and I can see the plots made by g_energy.
So how can I use g_energy to tell if my energy minimisation had indeed 
reached a minimum, if I can't compare potential energy and density as 
confusingly suggested in the speptide tutorial?



> 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
Sorry for the inconsistency

> 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.
the density will only be in the energy file when it is allowed to
fluctuate (i.e. constant pressure simulation). I don't remember whether
this is the case in the demo

> 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
search for grace

Groeten, David.
Dr. David van der Spoel, 	Dept. of Cell & Mol. Biology
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel

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

dan at chalkie.org.uk
white at cc.jyu.fi

More information about the gromacs.org_gmx-users mailing list