[gmx-users] position restraints

[Justin Lemkul]

On 3/25/13 1:40 PM, Shima Arasteh wrote:
> Believe me I add this line to mdp file as you wrote in KALP-15-DPPC.
>

I believe what I see.  If you're trying to re-type from memory what's in your 
topology and/or .mdp file, that's not productive.  Please copy and paste to make 
efficient use of everyone's time.

> "define        = -DPOSRES_LIPID"
>
> Also added these to top file.
> #ifdef POSRES_LIPID
> #include "lipid_posre.itp"
> #endif
>   But I get again this error that the "This probably means that you have inserted topology section "position_restraints"
> in a part belonging to a different molecule than you intended to."
>
> Why this doesn't match?? I think POSITION RESTRAINING is making me crazy! :((
> Would you please help me?
>

I've been trying, and it appears you're either giving inconsistent or incorrect 
information.  Copy and paste directly from your .top file whatever sections are 
relevant.  You also haven't said what is in lipid_posre.itp, which can be 
another source of problems.  You just said you've created it with genrestr, but 
you didn't say what group you included.  The numbering in the position restraint 
file is per [moleculetype], not the global atom numbering in the coordinate file.

-Justin

-- 
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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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