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. 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, li lin. ------------------- This email was sent at the request of a user - please do not respond to this email. -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
