[gmx-users] Multiple position restraints on the same system

[Justin A. Lemkul]

NG HUI WEN wrote:
> Dear GMXusers,
> 
>  
> 
> I am trying to perform NVT on my solvated protein-lipid system. After 
> inserting the protein into the lipid using inflategro and a round of 
> energy minimization, I performed a 100ps NVT with position restraint 
> only on the protein molecule using (posre.itp).
> 
>  
> 
> After 100ps of NVT, the bilayer separated. As a result, I am now trying 
> to redo the NVT step, this time probably with position restraints on the 
> protein AND the P8 atom of my POPC (lipid_posre.itp).
> 
>  
> 
> I have in my .top file
> 
> ;Protein
> 
> #include “protein.itp”
> 
> #ifdef POSRES
> 
> #include “posre.itp”
> 
> #endif
> 
>  
> 
> ;Lipid
> 
> #include”popc.itp”
> 
> #ifdef POSRES_LIPID
> 
> #include “lipid_posre.itp”
> 
> #endif
> 
>  
> 
> When it comes to the .mdp file, I wonder how do I include both
> 
> define = -DPOSRES and define = -DPOSRES_LIPID ?
> 

Yes, but not in two separate "define" statements.  The proper method is:

define = -DPOSRES -DPOSRES_LIPID

>  
> 
> Another quick question, is it advisable to do “trjconv –pbc mol” on my 
> system after every energy minimization/ MD to get an unbroken structure 
> before I carry on further?
> 

If the output structure is broken, then yes, you should make the molecules whole 
before any further InflateGRO, EM, or simulation steps.

-Justin

>  
> 
> Thanks a lot
> 
>  
> 
> HW
> 
>  
> 
> <<
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-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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