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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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
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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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