Fw: Fwd: [gmx-users] position restraints

[Justin Lemkul]

On 3/18/13 6:02 AM, Shima Arasteh wrote:
> 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?
>

Were restraints correctly applied?  Your last messages indicated fatal errors in 
trying to apply restraints - have you overcome those problems?  Is there a 
position restraint energy term written to the .log and .edr files?  Using such a 
huge force constant should not result in such RMSD values unless (1) they are 
not being applied or (2) whatever groups you have created for applying 
restraints do not cover all atoms that are being analyzed in the RMSD 
calculation, i.e. some are unrestrained and moving normally when you think they 
are being restrained.

-Justin

>
> 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
>>
>

-- 
========================================

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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