On 7/11/2010 4:14 AM, Martin Kamp Jensen wrote:
Hi Chris,
On Sat, Nov 6, 2010 at 5:58 PM, Krzysztof Mlynarczyk
<mitomas...@gmail.com <mailto:mitomas...@gmail.com>> wrote:
Hi,
You need to use md integrator for -rerun to work.
Aha, now it seems to work. Thanks!
I am just sad that I did not find that information. According to
http://manual.gromacs.org/current/online/mdrun.html "With -rerun an
input trajectory can be given for which forces and energies will be
(re)calculated. Neighbor searching will be performed for every frame,
unless nstlist is zero (see the .mdp file)."
Writing and documenting bulletproof software is tough work :-(
I've fixed the code so that -rerun and EM or NM integrators flag a fatal
error.
Mark
Good luck,
Chris
2010/11/6 Martin Kamp Jensen <martin.kamp.jen...@gmail.com
<mailto:martin.kamp.jen...@gmail.com>>
Hello,
Hopefully someone can help me understand how to use the mdrun
-rerun functionality, because currently I am confused. I would
like to be able to look up potential energy values for a
number of conformations by calling mdrun -rerun once.
The idea to use mdrun -rerun is from advice given to me by
Mark Abraham on the gmx-developers list
(http://lists.gromacs.org/pipermail/gmx-developers/2010-September/004731.html
and
http://lists.gromacs.org/pipermail/gmx-developers/2010-October/004770.html):
You want GROMACS to find the energy of a potentially
infinite set of coordinates that appear magically, and
that is what mdrun -rerun does.
The elegant way to do that is to write your series of
conformations to a pseudo-trajectory (in whichever of
GROMACS many trajectory formats is convenient to you), and
then invoke mdrun -rerun on that trajectory with a
suitable .tpr. Then you either parse the .log file or the
output .edr file for the energies.
I wanted to find out how this works so I have been
experimenting. I started out by looking at the Peptide
tutorial at
http://manual.gromacs.org/current/online/speptide.html. I used
three different mdp files (integrator = steep, nsteps = 0, 1,
2). This gave me three conformations and their energy values.
For testing purposes I then wanted to get the energy values
for those three conformations using mdrun -rerun (and since I
already have the correct energy values it is easy to verify
the results).
First, I created a trajectory by concatenating the three
conformations (gro files) into one gro file (which is okay
according to
http://manual.gromacs.org/current/online/gro.html: "gro files
can be used as trajectory by simply concatenating files"). I
then used an mdp file with integrator = steep and nsteps = 0
indicating that I just want the energy value (listed in the
output, in the log file or by using g_energy). Now, by using
mdrun -s <tpr file> -rerun <gro trajectory file> I only get
the energy value for the first conformation listed in the gro
file used to create the tpr file. The -rerun option does not
seem to have any effect at all.
I used the following commands three times to create three
different conformations (one conf_mdrun.gro file for each
time) with different energy values. I am just setting nsteps
to 0, 1, or 2 (integrator = steep) in em.mdp.
pdb2gmx -f speptide -o conf_pdb2gmx -p top_pdb2gmx -i
top_pdb2gmx << EOF
1
1
EOF
editconf -f conf_pdb2gmx -o conf_editconf -d 0.5
genbox -cp conf_editconf -cs -p top_pdb2gmx -o conf_genbox
mv top_pdb2gmx.top top_genbox.top
mv "#top_pdb2gmx.top.1#" top_pdb2gmx.top
grompp -f em -po em_grompp -c conf_genbox -p top_genbox -o
em_grompp
mdrun -s em_grompp -o mdrun -c conf_mdrun -e mdrun -g mdrun
I was hoping the following would give me the three energy
values for the three conformations in 2+1+0.gro, which is the
concatenation of the three conf_mdrun.gro files from before.
However, I just get the energy value from the first
conformation in the file. Using the -rerun option does not
make a difference (I can put whatever after -rerun, even files
that do not exist, without any effect).
grompp -f em -po em_grompp -c gro/2+1+0 -p top_genbox -o
em_grompp
mdrun -s em_grompp.tpr -rerun gro/2+1+0.gro
Regards,
Martin.
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Regards,
Martin.
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