[gmx-users] A question about positiont constraint

Mark Abraham Mark.Abraham at anu.edu.au
Tue May 29 07:09:13 CEST 2007

yang zaixing wrote:
> Dear Groamcs 
> user,                                                                              
> I'm trying to do something about peptides aggregation, but the timescale 
> is unendurable.         
> A paper has ever refered that by the using of position constraint can 
> greatly reduce the         
> timescale for the appearance of anti-parallel beta-sheet conformation of 
> peptides.               
> Now,i want to constraint the positions of the peptides 
> by                                        
> harmonic coupling [the spring constant, kc, is 0.03 kcal/(mol A° 
> )]                             
> between the center of the water box and the oligomer center of 
> mass.                             
> Does anyone know how to add this 
> constraint?                                                     

If it's not described in the relevant GROMACS manual section (and I 
don't think it is), then you'd have to write code inside GROMACS to do this.


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