[gmx-users] pull code

Poojari, Chetan c.poojari at fz-juelich.de
Wed Feb 9 16:18:01 CET 2011


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 ?????

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?????

Any suggestions will be helpful.

Kind regards,

Forschungszentrum Juelich GmbH
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Geschaeftsfuehrung: Prof. Dr. Achim Bachem (Vorsitzender),
Dr. Ulrich Krafft (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt,
Prof. Dr. Sebastian M. Schmidt

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