[gmx-users] fail to pull

Justin Lemkul jalemkul at vt.edu
Sun Apr 7 18:08:13 CEST 2013

On Sun, Apr 7, 2013 at 12:05 PM, Albert <mailmd2011 at gmail.com> 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 A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540)


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