Fw: Fwd: [gmx-users] position restraints

[Shima Arasteh]

With position restraints I got a new RMSD with the Min 0.05 and Max 0.11. I don't know if this range of deviation with position restraints is sensible or not! I can't believe with such a force of 100000 I still see deviations!

I'd prefer to get less deviation. Would it be possible by using a greater fc ? Is it sensible?


Thanks for your suggestions in advance.

 
Sincerely,
Shima


----- Original Message -----
From: Justin Lemkul <jalemkul at vt.edu>
To: Shima Arasteh <shima_arasteh2001 at yahoo.com>; Discussion list for GROMACS users <gmx-users at gromacs.org>
Cc: 
Sent: Saturday, March 16, 2013 12:24 AM
Subject: Re: Fw: Fwd: [gmx-users] position restraints



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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