[gmx-users] pull code

[Justin A. Lemkul]

Poojari, Chetan wrote:
> Hi Justin,
> 
> Thank you very much for your suggestions. I will use constraint force  to
> force a peptide into a membrane with pulling for longer time.
> 
> yes with "POSRES_LIPID"   i am keeping the lipids rigid while pulling the
> peptide inside.  Should the lipids be flexible while pulling??
> 

If your lipids are completely rigid, then they will not be happy accommodating 
the introduction of a peptide into that environment.

> I am using pull_geometry   = direction, In the tutorial mdp file you had
> commented saying cant get PMF with direction. So please can I know if this
> error of not getting PMF with direction fixed or with pull_geometry   =
> distance will i be able to pull the peptide into membrane with still using
> pull direction pull_vec1       = 0.0 0.0 -1.0
> 

You're not doing umbrella sampling, you're doing steered MD, which is a 
non-equilibrium process.  Please read the tutorial carefully.

-Justin

> 
> 
> 
> Kind regards, chetan
> 
> 
> ________________________________________ From: gmx-users-bounces at gromacs.org
> [gmx-users-bounces at gromacs.org] On Behalf Of Justin A. Lemkul
> [jalemkul at vt.edu] Sent: 09 February 2011 16:40 To: Discussion list for
> GROMACS users Subject: Re: [gmx-users] pull code
> 
> 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.
>> 
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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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-- 
========================================

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

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