[gmx-users] question regarding restraints

[David van der Spoel]

gurpreet singh wrote:
> Hello users
>  
> I am using the gromacs 3.3 with 43a1 force field.
> I am using a restraint force of 50 intially during the beginning of 
> protein simulation in water, even after such a high value of restraint 
> force i can see some major deviations in my structure during the 
> simulation.
>  
> My doubt is that since i am applying enough restrain force on the 
> protein it should not deviate at all from its native conformation.
> I want to know is this the usual behavior in gromacs or i am making some 
> mistake in  applying restrain.
>  
> I am using a posre.itp file using define = -dposre in the .mdp file for 
> applying the restraining force. 
>  

are you sure the restraints are applied? check whether you have an 
energy term corresponding to it. typical force constants people use are 
1000 kJ/mol/nm^2

>  
> With regards 
> Gurpreet
>  
> 
> 
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-- 
David van der Spoel, Ph.D.
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se