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

David van der Spoel spoel at xray.bmc.uu.se
Tue May 13 12:56:01 CEST 2003

On Tue, 2003-05-13 at 12:36, Dr. Daniel James White PhD wrote:
> 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

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