On Sun, Apr 7, 2013 at 12:05 PM, Albert <[email protected]> wrote:
> hello Justine: > > thanks a lot for such kind comments. > > I may find the problem, the COM probably is not suitable to use whole > protein since I found by g_dist that all the distance are between 0.9-1.0 > nm throughout the whole pulling process. > > BTW, I notice that we are using command: > > grompp -f md_pull.mdp -c npt.gro -p topol.top -n index.ndx -t npt.cpt -o > pull.tpr > > > for pulling .tpr generating. May I ask whey shall we use option > > "-t npt.cpt" > > in this step? Usually we only need to specify .mdp, .gro and .top file > for .tpr file.... > > I'm assuming you're getting that line from my tutorial. You pass the .cpt file to grompp to preserve velocities from the previous equilibration phase. If you don't, what was the point of equilibrating? Coordinates, topology, and .mdp parameters are all that are strictly required to produce a .tpr file, but other files may be necessary to produce a sensible .tpr file based on previous steps. -Justin -- ======================================== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ======================================== -- 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
