[gmx-users] polyalanine melt

li jianguo ljgsq at yahoo.com
Thu Jan 22 06:38:34 CET 2009

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,
Dept. Chemcial and Biomolecular Engineering
National University of Singapore


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