[gmx-users] polyalanine melt

XAvier Periole x.periole at rug.nl
Thu Jan 22 09:38:22 CET 2009

On Jan 22, 2009, at 6:38 AM, li jianguo wrote:

> 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?
I would indeed expect a polyalanine peptide to be mostly unstructured  
in solution.
I seem to me that the length of the polyalanine would be a very  
important factor
to the "structure" of the polyalanine peptide. I believe there is some  
data on this.
The force field you use is also important. For short peptide different  
FF would have
different propensity for helix/shift.
> Thanks very much,
> Jianguo
> Dept. Chemcial and Biomolecular Engineering
> National University of Singapore
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