[gmx-users] polyalanine melt

[Kukol, Andreas]

I have no experience with polyalanine, but you may try position restraint MD for longer (500 ps) and energy minimisation of the the whole system afterwards.

Andreas

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From: gmx-users-bounces at gromacs.org [mailto:gmx-users-bounces at gromacs.org] On Behalf Of li jianguo
Sent: 22 January 2009 05:39
To: gmx-users at gromacs.org
Subject: [gmx-users] polyalanine melt

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