[gmx-users] pull code

[Justin A. Lemkul]

Poojari, Chetan wrote:
> Hi,
> 
> I am using umbrella sampling to pull my peptide (peptide starting from above the lipid bilayer) into the hydrophobic core of the lipid bilayer.
> 
> Following are my inputs i have used:
> 
> title           = Umbrella pulling simulation
> define          = -DPOSRES_LIPID
> ; Run parameters
> integrator      = md
> dt              = 0.002
> tinit           = 0
> nsteps          = 250000        ; 500 ps
> nstcomm         = 1
> .
> .
> ; Pull code
> pull            = umbrella
> pull_geometry   = direction
> pull_dim        = N N Y
> pull_start      = yes           ; define initial COM distance > 0
> pull_ngroups    = 1
> pull_group0     = POPC
> pull_group1     = Protein
> pull_vec1       = 0.0 0.0 -1.0
> pull_rate1      = 0.01          ; 0.01 nm per ps = 10 nm per ns
> pull_k1         = 1000          ; kJ mol^-1 nm^-2
> 
> 
> After running the this step:  grompp -f md_pull.mdp -c npt.gro -p topol.top -n index.ndx -t npt.cpt -o pull.tpr
> 
> i get grompp output as such:
> 
> Pull group  natoms  pbc atom  distance at start     reference at t=0
>        0      6656      3433
>        1       105        53  -4.132                -4.132
> 
> I am starting to pull my peptide from 1nm above the upper leaf headgroup. I am using POPC lipids and distance between 2 adjacent headgroups seem to be around 4.2 nm.
> 
> I want the peptide to be pulled into the bilayer till the lower leaf lipid headgroups, but the peptide is being pulled only till middle of the hydrophobic core of the bilayer.
> 
> Please can I know what might be the problem ?????
> 

Either you're (1) not pulling for sufficient time, (2) not pulling hard enough, 
or (3) the physical properties of the system don't allow for such a position.

For (2), using a harmonic potential to try to force a peptide into a membrane is 
probably not a great idea.  A constraint force is probably better.  For (3), 
what does "POSRES_LIPID" refer to?  Are you keeping the lipids too rigid by 
doing so?

> 
> While viewing the conf.*gro file outputed  from the traj. (after extracting the frames), i found few lipid molecules to be broken. Please can I know if there is a way to avoid these broken structures??? Is there a possibility that I am not able to pull the peptide into the lower leaf head group due to these broken lipid structures?????
> 
> 

Please become comfortable with the concept of periodic boundary conditions.

http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions

-Justin

> 
> 
> Any suggestions will be helpful.
> 
> 
> Kind regards,
> chetan.
> 
> ------------------------------------------------------------------------------------------------
> ------------------------------------------------------------------------------------------------
> Forschungszentrum Juelich GmbH
> 52425 Juelich
> Sitz der Gesellschaft: Juelich
> Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498
> Vorsitzender des Aufsichtsrats: MinDirig Dr. Karl Eugen Huthmacher
> Geschaeftsfuehrung: Prof. Dr. Achim Bachem (Vorsitzender),
> Dr. Ulrich Krafft (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt,
> Prof. Dr. Sebastian M. Schmidt
> ------------------------------------------------------------------------------------------------
> ------------------------------------------------------------------------------------------------

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

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

========================================