[gmx-users] Gromacs multisubunit defragmentation
Muhammad Hagras
mahagras at ucdavis.edu
Tue Jun 14 19:13:30 CEST 2016
It actually worked now with the option pbc=no (I was previously just
commenting out pbc but it seems it is not the same as pbc=no!),
But with pbc=xyz, it does fragment! Weird! When playing with the box size,
I see different fragmentation patterns!
On Tue, Jun 14, 2016 at 10:09 AM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>
> On 6/14/16 12:45 PM, Muhammad Hagras wrote:
>
>> Thanks Justin for your help,
>>
>> I am also surprised from that subunit movements!
>>
>> Here are the commands that I used in sequence:
>>
>> 1- pdb2gmx_d -f protein.pdb -o protein.gro -p protein.top
>> 2- editconf_d -f protein.gro -o protein_pbc.gro -d 1.0
>> 3- grompp_d -v -f minim.mdp -c protein_pbc.gro -p protein.top -o
>> protein.tpr
>> 4- mdrun_d -v -deffnm protein -c protein_EM.pdb
>>
>>
> I don't see how this sequence would lead to any issues, with or without
> PBC. But in any case, for visualization purposes, just re-image using
> trjconv.
>
> -Justin
>
>
> Thanks for help,
>>
>> Muhammad
>>
>> On Tue, Jun 14, 2016 at 4:23 AM, Justin Lemkul <jalemkul at vt.edu> wrote:
>>
>>
>>>
>>> On 6/13/16 9:26 PM, Muhammad Hagras wrote:
>>>
>>> Hi folks,
>>>>
>>>> I need some help in running EM on three subunits protein (not covalently
>>>> bonded),
>>>>
>>>> When I run EM on such molecule in vacuum or in implicit solvent, the
>>>> three
>>>> subunits move apart ?! I tried with and without pbc and with and without
>>>> implicit solvent and still the same results!
>>>>
>>>>
>>>> That seems somewhat impossible. Without PBC, there is no box and
>>> therefore atoms/molecules don't jump. You're applying restraints, so
>>> there
>>> shouldn't be any really large movement. "Broken" molecules are due to
>>> PBC,
>>> so all you're seeing is the fact that with PBC, you haven't set up the
>>> box
>>> appropriately. But you haven't provided enough information (all commands
>>> up to this point, including how you set up the box), so it's a bit of a
>>> guess.
>>>
>>> -Justin
>>>
>>>
>>>
>>> Here is my minim.mdp I used
>>>> -------------------------------------------------------------------
>>>> title = Energy Minimization ; Title of run
>>>>
>>>> ; The following line tell the program the standard locations where to
>>>> find
>>>> certain files
>>>> cpp = /lib/cpp ; Preprocessor
>>>>
>>>> ; Define can be used to control processes
>>>> define = -DPOSRES
>>>>
>>>> ; Parameters describing what to do, when to stop and what to save
>>>> integrator = cg ; Algorithm (steep = steepest descent
>>>> minimization)
>>>> emtol = 10.0 ; Stop minimization when the maximum
>>>> force
>>>> < 1.0 kJ/mol
>>>> nstcalclr = 1
>>>> nstcgsteep = 10000
>>>> dt = 0.001
>>>> nsteps = 1000000000 ; Maximum number of
>>>> (minimization)
>>>> steps to perform
>>>> nstenergy = 10000 ; Write energies to disk every nstenergy
>>>> steps
>>>> energygrps = System ; Which energy group(s) to write to disk
>>>> ;freezegrps = Backbone
>>>> ;freezedim = Y Y Y
>>>> rlist = 1.0
>>>> lincs_order = 8
>>>> lincs_iter = 4
>>>> nstcomm = 1
>>>> nstcalcenergy = 1
>>>> cutoff-scheme = group
>>>>
>>>> comm_mode = Linear
>>>> ;nstcomm = 1
>>>> ;dispcorr = EnerPres
>>>> ;optimize_fft = yes
>>>> ;pme_order = 6
>>>> ; Parameters describing how to find the neighbors of each atom and how
>>>> to
>>>> calculate the interactions
>>>> ns_type = grid;simple ; Method to determine neighbor list
>>>> (simple, grid)
>>>> coulombtype = PME;cut-off ; Treatment of long range electrostatic
>>>> interactions
>>>> vdwtype = cut-off
>>>> rcoulomb = 1.0 ; long range electrostatic cut-off
>>>> rvdw = 1.0 ; long range Van der Waals cut-off
>>>> ;constraints = all-bonds ; Bond types to replace by
>>>> constraints
>>>> pbc = xyz ; Periodic Boundary Conditions (yes/no)i
>>>>
>>>>
>>>> ; IMPLICIT SOLVENT ALGORITHM
>>>> implicit_solvent = no;gbsa
>>>>
>>>> ; GENERALIZED BORN ELECTROSTATICS
>>>> ; Algorithm for calculating Born radii
>>>> gb_algorithm = Still;OBC
>>>> ; Frequency of calculating the Born radii inside rlist
>>>> nstgbradii = 1
>>>> ; Cutoff for Born radii calculation; the contribution from atoms
>>>> ; between rlist and rgbradii is updated every nstlist steps
>>>> rgbradii = 1.0
>>>> ; Dielectric coefficient of the implicit solvent
>>>> gb_epsilon_solvent = 4
>>>> ; Salt concentration in M for Generalized Born models
>>>> gb_saltconc = 0
>>>> ; Scaling factors used in the OBC GB model. Default values are OBC(II)
>>>> gb_obc_alpha = 1
>>>> gb_obc_beta = 0.8
>>>> gb_obc_gamma = 4.85
>>>> gb_dielectric_offset = 0.009
>>>> sa_algorithm = Ace-approximation
>>>> ; Surface tension (kJ/mol/nm^2) for the SA (nonpolar surface) part of
>>>> GBSA
>>>> ; The value -1 will set default value for Still/HCT/OBC GB-models.
>>>> sa_surface_tension = 2.25936
>>>>
>>>> -----------------------------------------------------------------------
>>>>
>>>> Thanks for help,
>>>>
>>>> Muhammad Hagras
>>>> PhD, Biophysics UCD
>>>>
>>>>
>>>> --
>>> ==================================================
>>>
>>> Justin A. Lemkul, Ph.D.
>>> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>>>
>>> Department of Pharmaceutical Sciences
>>> School of Pharmacy
>>> Health Sciences Facility II, Room 629
>>> University of Maryland, Baltimore
>>> 20 Penn St.
>>> Baltimore, MD 21201
>>>
>>> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
>>> http://mackerell.umaryland.edu/~jalemkul
>>>
>>> ==================================================
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> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==================================================
> --
> Gromacs Users mailing list
>
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