Hi,
I am new to Amber. I have to run > 5ps simulation on dna sequences with
12bp.
The details of my simulation protocol are same as that in the tutorial,
except for PME cutoff (14.0) and that for production run I have divided the
whole trajectory equal parts of 800ps.
The problem is that after sometime (which is different for different runs)
dna reaches the edge of the box in the reimaged trajectory.
The Energies, Temperature, pressure, density, volume all converge. The rmsd
also converges to value < 3.
I tried by increasing the time for restrained minimization and MD in the
equillibriation run which provided me with some success, however after 3.6
ns the DNA again reaches the edge of the box.
I have tried different reimaging methods but with no success.
I know that if the molecule goes out of the box the it may be interacting
with its image. Is it always the case? Is there any way to know this for
sure?
This can also be due to translation and rotation of DNA even if it is not
interacting with its image.
If this is the case, is the trajectory still meaningful for drawing
conclusions?
The edges of the box are 8.0 angstroms from DNA in the initial coordinates.
Increasing it is the last option for me.
I have not changed the nscm parameter yet. Can its value be less than the
time step for writing the coordinates of the snapshots?
Thanks in advance,
--
....for afterwards a man finds pleasure in his pains,
when he has suffered long and wandered far.
-Homer
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Received on Wed Mar 16 2011 - 04:00:01 PDT
