Protein distort during equilibration

From: snoze pa (
Date: Mon Jun 13 2011 - 10:22:10 CDT

Dear NAMD users,

 I am in a strange situation. First I equilibrated protein using harmonic
constraint. During that the whole system was equilibrated up to 500 ps. Next
I try to release the harmonic constraint and further equilibrate the system
for 1ns. This time part of the protein got distorted. Do you have any clue?
I have limited computer resources and it takes time to get that time scale
for my system which is ~300,000 atoms. I am running water in box simulation.

Thank you very much for your help.


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