[gmx-users] question about getting the same potential

linbingbing0214 at sina.com linbingbing0214 at sina.com
Fri Feb 24 12:54:48 CET 2012

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.
  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.   
  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,

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