Fw: Fwd: [gmx-users] position restraints

[Shima Arasteh]

Dear users,


Although I put the position restraints on backbone, I get RMSD around 0.2 nm. Is it usual? 
This deviation is just for a minimization step only. I' m on doubt about keeping the backbone in a fix secondary structure.
I' d prefer to restraint the backbone completely. Is it possible?

Thanks in advance.



Restraints allow, by definition, for slight deviations.

Erik
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Dear gmx users,

I want to use restraints on backbone of my protein to keep its secondary
 structure during minimization and equilibration steps. To do so, I 
generated backbone-restrain.itp and then included it to top file. Next, 
added define = -DPOSRES to minim.mdp file.
After minimization, when I check the minimization output file, I saw 
that the backbone of input and output files are not exactly the same.
Is there any step which I have not done to set the restraints correctly?


Thanks in advance.

Sincerely,
Shima