[gmx-users] several basic questions on GROMACS

Brett brettliu123 at 163.com
Tue Apr 5 15:24:26 CEST 2016

Dear All,

Based on the on-line Lysozyme tutorial, I started a MD from energy minimization to NVT equlibation to NPT equlibration, and I am now in the production MD step.

When I checked my Directory containing all the MD files for the whole MD process, I find there is a "mdout.mdp". Is my understanding correct on that, in the energy minimization step, it will create a "mdout.mdp" file, and in any of the following of NVT equlibation, NPT equlibration and production MD step, a "mdout.mdp" file will be created and automatically replaced the "mdout.mdp" file created in the previous step?

As I mentioned, currently I was in the production M step, and if I intentionally delete the "mdout.mdp" file from the Directory, how does it affect my production MD?

The next question, during my production MD step, I checked my Directory, and here let me take the NVT related files as example, I found there were a nvt.cpt and a nvt_prev.cpt file. Suppose my NVT equilibration step lasts for 100 ps, is the nvt.cpt the file created by "gmx grompp -f npt.mdp -c nvt.gro -t nvt.cpt -p topol.top -o npt.tpr", and the nvt_prev.cpt the cpt file created at the end of "gmx mdrun -deffnm npt -v &", and this nvt_prev.cpt file will be used at the beginning of the next step NPT equilibration?


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