[gmx-users] energy terms in following runs
spoel at xray.bmc.uu.se
Wed Feb 19 21:55:31 CET 2003
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?
> > 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
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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