[gmx-users] position_restraint anfd full Dynamics and berendsen Nose hoover Thermostat

shahid nayeem msnayeem at gmail.com
Wed Apr 7 13:08:18 CEST 2010

Dear users
Please let me know some basic question. I am sorry if I am asking a silly
a) While simulating a protein thermal unfolding at high temperature say 500K
should I run position restraint dynamics at 500k or at 298K. I am doing
100ps position restraint dynamics at 500k. Am I right in doing so.
b) While using Berendsen thermostat, how to select a value of tau_t and how
does it affects simulation output. The same question for NoseHoover
c) After completing the 100ns simulation when I view the .xtc file in VMD I
find that  alpha helix of the protein is unfolded in very first frame
collected at 10ps interval and reduced by trjconv  at 50ps interval. Is it
possible. If not then where I am wrong.
I did Steepest descent minimization, then 100ps position restraint Dynamics
at 500K and then 100ns full dynamics at 500k.
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