Hi, In molecular dynamics I have learned that there are three main phases: energy minimization, equilibration (say, 2 ns in duration), and production/dynamics (say, 3 ns in duration). Suppose that I want my production run to use the same conditions as equilibration. What is the best way to do this?
I can think of two conceptual ways to approach this: (1) Do one long 5 ns run. Then, when doing analysis, ignore the frames corresponding to the initial 2 ns, using the -b option found in most of the Gromacs trajectory analysis programs to consider only the final 3 ns. (2) Do equilibration and production in separate runs. This way, doing analysis is perhaps more foolproof: I don't need to worry about always neglecting the initial 2 ns, and the initial time I consider is always, conveniently, t = 0 ps. >From looking at various Gromacs tutorials, it seems that approach (2) is recommended. But now, even within approach (2), there are at least two options. One option is to feed the checkpoint file from equilibration into the grompp part of production. For example, EQUILIBRATION: [equilibration has been prepared using grompp] mdrun -deffnm npt-eq -cpo npt-eq.cpt PRODUCTION: grompp -f npt-md.mdp -c npt-eq.gro -t npt-eq.cpt -p water.top -o npt-md.tpr -po npt-mdout.mdp mdrun -deffnm npt-md where I have used the -cpo option in mdrun of equilibration and fed this resulting checkpoint file to grompp of production, using -t. Is this correct? Or, I could eliminate the grompp step of production (since my production run uses the same parameters as in equilibration) and feed the checkpoint file directly to mdrun of production: EQUILIBRATION: mdrun -deffnm npt-eq -cpo npt-eq.cpt PRODUCTION: mdrun -deffnm npt-md -cpi npt-eq.cpt where I have used -cpi in mdrun of production to feed in the checkpoint file. (In contrast to grompp, there is no -t option in mdrun.) Is this correct? My concern here is that, in the entry for mdrun in the Gromacs manual, it says that for the option -cpi, "By default the output will be appending to the existing output files." But since I have specified output file names using -deffnm npt-md, will the trajectory indeed be written to npt-md files, or will it be appended to the npt-eq files, from which the checkpoint file originated? If both of these options are correct, which is preferable? Thank you very much. Andrew DeYoung Carnegie Mellon University -- 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
