On 24/02/2012 7:05 PM, [email protected] wrote:
li lin wants to a share a link on the Gromacs wiki:
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List/Search
li lin says:
Dear all,
Recently I made some tests, and I want to get same potential with the
following method. (gmx 4.0.5.)
Firstly, I run a complete simulation as the reference. Then I got a log file.
Secondly, I use trjconv(-sep) to get each frame to a separate *.gro file.
The .gro files have different coordinates (i.e. at lower precision) than
existed during the simulation.
Thirdly, I use *.gro and run md for just one step (delta t=2fs), and another
input files are same with the reference one. Then I just want to read potential
in step 0 in the log file.
There are also issues with constraints. You should use mdrun -rerun on
the trajectory file to recompute energies without modifying the
coordinates in that trajectory - but note that the .xtc is also at
reduced precision compared with the original simulation.
Mark
I compare the potential which I got from different log files, and I found that there
are big difference between them. But in my opinion, as they have the same structure and
topol.top they should have the same (or little difference) Energies
like"G96Angle, Proper Dih., Improper Dih., LJ-14, Coulomb-14, LJ (SR), Disper.
corr., Coulomb (SR), Coul. recip., and Potential".
The following is the job script lines :
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
# Reference
grompp -f md.mdp(nsteps=50000) -c npt.gro -t npt.cpt -p topol.top -o md.tpr
mpirun -np 8 mdrun_mpi -deffnm md
# Comparison
echo 0|trjconv -f md.xtc -s md.tpr -o ./md_gro/md.gro -sep -pbc mol -ur
compact
grompp -f md1.mdp(nsteps=1) -c ./md_gro/mdi.gro(i=0,1,...) -p topol.top -o
./tpr/md_1_i.tpr
mpirun -np 8 mdrun_mpi -s ./tpr/md_1_i.tpr -g ./log/md_1_i.log
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Do you have some further ideas?
Thanks in advance!
best wishes,
li lin.
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