[gmx-users] pull code
Justin A. Lemkul
jalemkul at vt.edu
Mon Feb 14 16:55:05 CET 2011
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-bounces at gromacs.org [gmx-users-bounces at gromacs.org] On Behalf Of Justin A. Lemkul [jalemkul at 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-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.
>>>
>>> ------------------------------------------------------------------------------------------------
>>>
>>> ------------------------------------------------------------------------------------------------
>>> 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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