sharada wrote:
*Thankyou for the reply Mark. In fact I started another simulated
annealing job for my peptide with Tcoupl = Berendsen using the same
annealing protocol. I didnot get any warnings. However the temperature
increases from 0 to 53K and fluctuates around that through out till the
end of the simulation. I am attaching the Averages and RMS values for
the various components that its calculating. As you can see the average
Temp is around 56 -58. Why is this not increasing beyound that? I would
also like to know if the RMS fluctuations are in the required range ,
further if the system is behaving as an NVE ensemble which I don't
intend to do right now what parameters I should correct in order to
achieve an NPT ensemble. Density of methanol is maintained, however the
box sizes are reduced slightly from (editconf -f 2MLT_pdb2gmx.gro -o
2MLT_box.gro -bt octahedron -box 6.9 6.9 6.9) to the ones as shown
below. Kindly guide me through.
Read the manual sections in chapter 7 on simulated annealing and
temperature coupling, and check carefully how they work and what values
you've selected.
Mark
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