[gmx-users] li lin wants to share a link | Gromacs

Mark Abraham Mark.Abraham at anu.edu.au
Fri Feb 24 09:21:54 CET 2012

On 24/02/2012 7:05 PM, rossen at kth.se 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.


>    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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