[gmx-users] Gromacs multisubunit defragmentation
Justin Lemkul
jalemkul at vt.edu
Tue Jun 14 19:18:16 CEST 2016
On 6/14/16 1:13 PM, Muhammad Hagras wrote:
> 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!
>
This implies that the box is not set up correctly. Using -d 1.0 should have
taken care of this. If you're still getting broken things, then you're not
doing something right.
-Justin
> 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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>> * Please search the archive at
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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
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