Poojari, Chetan wrote:
Hi Justin,
As discussed earlier, I removed the restraints from lipids and used constraint
force for pulling, I was able to pull the peptide to the lower leaf headgroups
starting from 1.3nm above the upper leaf headgroups. Below is the pull code
inputs i used:
; Pull code
pull = constraint
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 = 0.013 ; 0.01 nm per ps = 10 nm per ns
pull_k1 = 1000 ; kJ mol^-1 nm^-2
But going through the summary_distances.dat file i wasnt sure of the
progression of COM distance between peptide and bilayer.
The first conf.gro starts at 3.84685nm it goes on reducing till it reaches conf
322 ........ 1.0903 nm, at this point when i viewed the 322.gro file the
peptide is approximately in center of the bilayer. From this point onwards
distance keeps increasing and it reaches conf 500 at 2.864 nm. But viewing the
gro. file in vmd from conf 328...... conf 500, the peptide is being pulled to
the lower leaf headgroups. So the peptide was pulled to the lower leaf
headgroup as expected but I am not sure with the progression.
0 3.8468513
1 3.8324797
2 3.8197916
.
.
.
322 1.0903752
.
.
328 1.1572036
.
.
498 2.8465521
499 2.8731604
500 2.8649662
From here i carried on to do umbrella simulations for 24 windows which i
generated for 10ns each, below is the pull code which i used for umbrella
sampling........after analysis PMF converges and looking at the histogram
theres sufficient overlap between windows. But due to increase in progression
after conf 322 till conf 500 some peaks in the histogram looks like written
twice.
; Pull code
pull = umbrella
pull_geometry = distance
pull_dim = N N Y
pull_start = yes
pull_ngroups = 1
pull_group0 = POPC
pull_group1 = Protein
pull_init1 = 0
pull_rate1 = 0.0
pull_k1 = 1000 ; kJ mol^-1 nm^-2
pull_nstxout = 1000 ; every 2 ps
pull_nstfout = 1000 ; every 2 ps
You've got a scenario for which the tutorial's input files will not suffice for
your purposes. The simple example in the tutorial is for a linear pull
resulting in a continually increasing COM distance. In your case, you are
starting at a relative positive COM displacement, and ending at a negative one
(i.e., below the POPC COM). For this application, you'll need to use a
different pull_geometry (probably "position"), and perhaps other options. There
are examples in the list archive, if you spend some time searching.
-Justin
Kind regards,
chetan
________________________________________
From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] On Behalf
Of Justin A. Lemkul [jalem...@vt.edu]
Sent: 10 February 2011 12:33
To: Gromacs Users' List
Subject: Re: [gmx-users] pull code
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-boun...@gromacs.org
[gmx-users-boun...@gromacs.org] On Behalf Of Justin A. Lemkul
[jalem...@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.
------------------------------------------------------------------------------------------------
------------------------------------------------------------------------------------------------
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
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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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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
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