[gmx-users] peptide insertion in lipid bilayer

[Justin A. Lemkul]

Moutusi Manna wrote:
> 
> Dear Justin,
>                  i am trying to insert a peptide in trans-bialyer 
> orientation into a pre-equilibrated POPC bilayer using  *inflategro* 
> <http://moose.bio.ucalgary.ca/files/inflategro> script. After 13 steps 
> of compression, the area per lipid is 2.61956768363491 nm^2, whereas the 
> desired area per lipid is 0.658 nm^2. But when i try to energy minimize 
> the compressed structure after 13th steps of compression, the energy did 
> not converged and give the following errors. During em i use strong 
> position restraints on peptide heavy atom using force constants of 100000.
> ------------------------------
> perl inflategro em_13.gro 0.95 POPC 0 com_13.gro 5 area_lip.dat
> grompp -f enermin.mdp -c com_13.gro -p system.top -o em_14.tpr
> mdrun -s em_14.tpr -nice 4 -o em_14 -c em_14 -e em_14 -g em_14&
> Reading file em_14.tpr, VERSION 3.3.1 (single precision)
> Steepest Descents:
>    Tolerance (Fmax)   =  1.00000e+03
>    Number of steps    =        50000
> 

<snip>

 From the LINCS warnings, you have a nice listing of where problems are 
occurring in terms of atom numbers.  Have a look at the structure and see what's 
causing the clash; that may help in diagnosing what's going wrong.

> 
> Steepest Descents converged to machine precision in 43 steps,
> but did not reach the requested Fmax < 1000.
> Potential Energy  = -1.2865473e+05
> Maximum force     =  4.7082656e+04 on atom 547
> Norm of force     =  6.7057188e+04

<snip>

> ---------------
> should i continue further compression with this energy minimized 
> structure (em_14.gro)??

Try it and see.  The forces don't look astronomical (they're high, but perhaps 
further EM can resolve them).  Furthermore, the LINCS warnings didn't indicate 
major changes in the constraint lengths.

-Justin

> if not how can i slove this problem.
> waiting for ur suggestion.
> Moutusi Manna
> 
>  
>  
> 
>  
> 
> 
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-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
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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