[gmx-users] energy terms in following runs

[David]

On Wed, 2003-02-19 at 16:39, Ester Chiessi wrote:
> 
> 
> David van der Spoel wrote:
> 
> > On Wed, 2003-02-19 at 14:42, Ester Chiessi wrote:
> > > Thanks for your answer.
> > >
> > > I verified ( with g_energy ) that there are small differences ( ranging from
> > > about 0.3 to 1 percent ) in every energy terms, except Coulomb(1-4).
> > > The bond term is different, too; I'm using SHAKE to fix distances only for
> > > hydrogen atoms.
> > Are you using xtc?
> 
> No.
> 
> > In that case energies will be different due to
> > roundoff in the coordinates. Otherwise you should doublecheck that
> > unconstrained start is on (in md.log)
> > and that you are not generating velocities (but tpbconv does not do
> > this).
> 
> In md0.log I read:bUncStart = FALSE
> 
> To prepare the second run, I used grompp giving in -c the last .gro file of the
> first run.
You don't need grompp to prepare the second run if it is a real
continuation of the previous:
tpbconv -s run1.tpr -f run1.trr -extend 1 -o run2

will make a run2.tpr which extends the previous run by 1 ps.

As Anton suggested, double check the md.log of the second run has 
bUncStart = TRUE
-- 
Groeten, David.
________________________________________________________________________
Dr. David van der Spoel, 	Dept. of Cell and Molecular 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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