[gmx-users] MD - analysis

[Kavyashree M]

Dear Sir,


> What does gmxcheck tell you about the .edr file that is giving weird
> results? Do the plots look normal?  Perhaps a frame got corrupted somewhere
> along the way.  The screen output should print how many frames were
> considered in the analysis; if it does not match your expectations based on
> nstenergy and the length of the simulation then something went wrong.


gmxcheck gave proper number of frames corresponding to 100ns, other plots
temp, pressure, volume, density look fine


> Most analyses do not need re-imaging.  Keeping the protein within the
> confines of one unit cell is typically just a convenience for visualization.
>

Ok.

I had done simulations of four similar protein using the same mdp file. in
one of them
the minimum distance between the periodic images went near 0.9nm, I had used
1.0nm
as distance between protein atoms and box wall. and cut offs were 1.0nm for
vdw and 1.4nm
for columb. Till some 17ns the minimum distance was above 2nm the gradually
there was a
dip after around 20-25ns. Now I ran 100ns simulation and I have to discard
this trajectory
because of this error. I thought distance of 2nm between protein atoms was
enough as 1.4nm
was the max cutoff.

How can we know prior to starting the simulation that we may get some such
errors for using
such a parameter. I could have used larger box size but it will increase the
time. Is it trial and
error basis to find out the optimum box size?

Thank you
With regards
M. Kavyashree
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