question regarding simulated annealing

From: Puspita Halder (
Date: Tue Aug 28 2012 - 07:03:39 CDT

Dear NAMD users,

I have a question regarding the water density in the solvation box during a
simulated annealing run. I have started the simulated annealing run of my
protein from a structure taken from a high temperature (500K) trajectory of
the same generated after the minimization, heating and md run for ~2 ns at
500K temperature under NPT condiition. I decreased the temperature of my
system staring from 500 K to 300 K in 5K temperature steps and for each and
individual temperature step I equilibrated the system for 100 ps and
finally equilibrated the system at 300K for 2 ns under NVT condition. The
annealing run was seemed to be ok from the log file . The only problem that
I found is the water density around the protein in the solvation box. This
is found to be kind of inhomogeneous means in some portion of the box water
is more dense whereas in the other portion it is less dense though the
protein remains always solvated . Is this due to the effect of temperature
decrease or something else? I have checked the xst file for the dimension
of the box and it was fixed.

If you need my config file for the simulated annealing run I'd send that.

If anyone of you have any clue regarding this please let me know.

Thanks for your help in advance.


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