[gmx-users] Rerun same trajectory - Pulling

Justin Lemkul jalemkul at vt.edu
Tue Dec 25 14:28:04 CET 2012

On 12/25/12 3:51 AM, Steven Neumann wrote:
> Maybe I wrote it wrote it wrong.
> I have 1500 frames of which with 0.1 nm spacing I have chosen 14 to
> run umbrella sampling windows.
> I used:
> conf0.gro
> conf140.gro
> conf213.gro
> conf262.gro
> conf263.gro
> conf300.gro
> ...
> conf1500.gro
> However, the moment when my ligand became dettached is very short
> (beween conf conf262.gro and 263.gro) that there is a gap in
> histograms. So I need the same pulling trajectory but with more frames
> e.g. 10 times higher.
> when I use grommp -f new.mdp -o new.tpr
> mdrun -rerun oldPull.xtc -s new.tpr -deffnm new
> I dont get my new.xtc ... Hoiw can I solve it?

Because, as I said, that's not what the -rerun function does.  The -rerun 
function simple re-evaluates the energies of the existing frames according to 
the topology in the .tpr file, thus allowing you to re-calculate energy terms 
based on new energy groups or a modified topology.  If a frame does not exist, 
you cannot create it magically.  If you didn't save the frame you needed, you 
need to run a new simulation.  There is no way to interpolate new frames.



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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