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
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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