Fw: Fwd: [gmx-users] position restraints

[Justin Lemkul]

On 3/15/13 8:50 AM, Shima Arasteh wrote:
> Dear users,
>
>
> Although I put the position restraints on backbone, I get RMSD around 0.2 nm. Is it usual?

No, 0.2 nm is very high.  With position restraints, offhand I would think around 
0.05 nm or less would be indicative of proper restraints.

> 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?
>

Yes, using genrestr to create a suitable posre.itp file that includes only 
backbone atoms.

-Justin

> Thanks in advance.
>
>
>
> Restraints allow, by definition, for slight deviations.
>
> Erik
> * Please don't post (un)subscribe requests to the list. Use thewww interface or send it to gmx-users-request at gromacs.org.
>
>
>
>
> 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
>

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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