[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
> as described in
> 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
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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