AW: question regarding simulated annealing

From: Norman Geist (
Date: Thu Aug 30 2012 - 01:50:11 CDT



I could imagine that the NPT run with a temperature of 500K generates
slightly other box dimensions as with 300K. So maybe you would have to NPT
again under the 300K conditions.


Norman Geist.


Von: [] Im Auftrag
von Puspita Halder
Gesendet: Dienstag, 28. August 2012 14:04
Betreff: namd-l: question regarding simulated annealing


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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