Mark Abraham Mark.Abraham at anu.edu.au
Fri Feb 13 23:19:48 CET 2009

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.


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