[gmx-users] Fwd: self-assembly and box size
Mohsen Ramezanpour
ramezanpour.mohsen at gmail.com
Tue Nov 15 03:43:03 CET 2016
On Mon, Nov 14, 2016 at 7:27 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>
> On 11/14/16 9:04 PM, Mohsen Ramezanpour wrote:
>
>> Thanks Justin for your comments.
>>
>> Comments interspersed.
>>
>> On Mon, Nov 14, 2016 at 6:47 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>>
>>
>>>
>>> On 11/14/16 5:11 PM, Mohsen Ramezanpour wrote:
>>>
>>> Dear Gromacs users,
>>>>
>>>> I have made an initial system with a number of molecules in a "large"
>>>> box.
>>>>
>>>> Large means a box of size 50 50 50 nm?
>>>>
>>>> I am interested in the self-assembly process of molecules (parametrized
>>>> in
>>>> charmm36 ff) in the box.
>>>>
>>>> I expected pressure coupling to shrink the box quickly, but it seems it
>>>> fails to do so. The simulation box did not change (ca. 0.5 nm in each
>>>> direction) which seems strange to me.
>>>>
>>>> I have used four different P-couple schemes for 4 different type of
>>>> self-assemblies:
>>>>
>>>> 1) isotropic
>>>>
>>>> pcoupl = berendsen
>>>> pcoupltype = isotropic
>>>> tau_p = 5.0
>>>> compressibility = 4.5e-5
>>>> ref_p = 1.0
>>>>
>>>>
>>>> 2) semiisotropic
>>>>
>>>> pcoupl = berendsen
>>>> pcoupltype = semiisotropic
>>>> tau_p = 5.0
>>>> compressibility = 4.5e-5 4.5e-5
>>>> ref_p = 1.0 1.0
>>>>
>>>>
>>>> 3) anisotropic with *fix shape* of box (*but the size could change*)
>>>>
>>>> pcoupl = berendsen
>>>> pcoupltype = anisotropic
>>>> tau_p = 5.0
>>>> compressibility = 4.5e-5 4.5e-5 4.5e-5 0 0 0
>>>> ref_p = 1.0 1.0 1.0 0 0
>>>> 0
>>>>
>>>> 4) anisotropic with *both size and shape able to change*
>>>>
>>>>
>>>> pcoupl = berendsen
>>>> pcoupltype = anisotropic
>>>> tau_p = 5.0
>>>> compressibility = 4.5e-5 4.5e-5 4.5e-5 4.5e-5 4.5e-5 4.5e-5
>>>> ref_p = 1.0 1.0 1.0 0 0 0
>>>>
>>>>
>>>> Here are some other parameters in mdp file which might be useful for
>>>> finding the problem:
>>>>
>>>> integrator = md
>>>> dt = 0.002
>>>> nsteps = 50000
>>>> nstlog = 1000
>>>> nstxout = 1000
>>>> nstvout = 1000
>>>> nstfout = 1000
>>>> nstcalcenergy = 100
>>>> nstenergy = 1000
>>>>
>>>> cutoff-scheme = Verlet
>>>> nstlist = 20
>>>> rlist = 1.2
>>>> coulombtype = pme
>>>> rcoulomb = 1.2
>>>> vdwtype = Cut-off
>>>> vdw-modifier = Force-switch
>>>> rvdw_switch = 1.0
>>>> rvdw = 1.2
>>>>
>>>> tcoupl = berendsen
>>>> tc_grps = Molecules water_ions
>>>> tau_t = 1.0 1.0
>>>> ref_t = 355 355
>>>>
>>>> constraints = h-bonds
>>>> constraint_algorithm = LINCS
>>>> continuation = yes
>>>>
>>>> nstcomm = 100
>>>> comm_mode = linear
>>>> comm_grps = Molecules WI
>>>>
>>>>
>>>> You shouldn't reset COM motion like this.
>>>
>>
>>
>> Do you mean deviding it to Molecules and WI? If yes, could you please let
>> me know why it is not approperiate?
>> How if I use "system" instead?
>>
>>
> Use System. Only layered systems should be considered for separate
> comm_grps. Your approach risks the different groups having spurious
> contributions from COM motion removal causing them collide. I've seen
> crashes from it before.
Sure. I will. I used this because I expected these lipids to eventually
form a bilayer or HII phase.
>
>
>
>>>
>>> refcoord_scaling = com
>>>
>>>>
>>>> gen-vel = no
>>>>
>>>> I can make the initial system smaller, but I think starting from a large
>>>> box would be better because it gives all the molecule enough freedom to
>>>> move and assemble in better way.
>>>>
>>>> Is not it right to expect the p-couple shrink the box in nanoseconds?
>>>> This
>>>> was only for 100 ps but I expected more shrinkage of box. What do you
>>>> think?
>>>>
>>>>
>>>> 100 ps is nothing.
>>>
>>>
>> Even if the box is not full with waters and there are a lot of empty
>> spaces
>> between molecules?
>>
>>
> "A lot" is subjective, but in general, I stand by the statement that 100
> ps is nothing in this context.
Agreed. Sorry for that. I think the example of 10*10*10 nm makes it clear
now. The system had about 200 lipids and 50 waters/lipids.
>
>
>
>>> If you have a box full of water, as your settings above imply,
>>>
>>
>> That is not the case, I have molecules and water, but there are plenty of
>> empty spaces.
>>
>>
> What is the purpose of void space? You're potentially introducing a lot
> of artificiality. Perhaps you need to better explain your goals. Using
> such a huge box is computationally very expensive, for potentially little
> or no gain, plus the headaches associated with bizarre behavior due to
> voids (which can also cause crashes).
Your right. Based on the number of lipids (200 is reasonable) an water
molecules I did not expect it to take too much time to fill these voids. I
will make it smaller.
>
>
>> you can't expect much of a change. Why do you need the box to shrink, or
>>> why do you expect it to?
>>>
>>
>>
>> Based on the number of lipid molecules and waters I added to the box, and
>> since the same system (with the same number of molecules and waters) will
>> be in lamellat or other phases (in equilibrium) of smaller sizes (e.g. 10
>> 10 10 nm). i.e. if I make a bilayer out of these, it will be ca.
>> 10*10*10
>> nm^3 in size
>>
>>
>> A box will only shrink a lot if there is substantial void space, e.g.
>>> intentional or due to a poor initial approximation of the system that
>>> requires equilibration.
>>>
>>> Agreed. Regarding what I described about the system, do you think this is
>> because 100 ps is not enough? Even for a small shrink of ~ 2 nm?
>>
>>
> Impossible to predict. But again, 100 ps is not nearly enough time to
> assess anything like what you're after.
Sure, I will run longer But for smaller box as you suggested.
Thanks for your comments Justin.
>
>
> -Justin
>
> --
> ==================================================
>
> 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
>
> * Please search the archive at http://www.gromacs.org/Support
> /Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>
--
*Rewards work better than punishment ...*
More information about the gromacs.org_gmx-users
mailing list