Dear all,
I am running MD simulaiton using Gromacs for alpha-helilx polyalanine solution.
The initial configuraiton of polyalanine peptide was generated using Discovery
Studio. I follow the procedure below:
1: solvate the polyalanine in a water box
2: energy minimization (steep for 5000 steps and cg for some steps until
convergence)
3: position restraint MD for 200 ps in NVT
4: position restraint MD for 200 ps in NPT
After that, I run MD simulation. The strange things is that the
alpha-helix polyalanine melt during MD simulation, and it became random coil
after several nano seconds.
Did any one encount such problem?
Thanks very much,
Jianguo
Dept. Chemcial and Biomolecular Engineering
National University of Singapore
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