[gmx-users] Prevent protein rotation - rectangular box

Wed Jun 4 04:14:13 CEST 2014

Thanks, unfortunately I have such restrictions.

I have defined two atoms which I wish to be dummy in my system. I placed
one in between 2 beta sheets on the one termini of my protein and copy it
moving along the z axis to the other beta sheet. I found closest prtoein
heavy atoms and made constraints with 2 dummy atoms. In my topology :

atomtypes.atp

DUM    0.0000   ; Dummy atom

ffnonbonded.itp (Charmm so all vdwd are turnedd of with them)

DUM    1    00.0000    0.00    V    0.0000000    0.0000000

aminoacids.rtp

[ DUM ]
 [ atoms ]
        DUM       DUM      0.0  0

Then, after pdb2gmx I add both constraints between dummies and closest
protein heavy atoms (4 or 6) and add:

 [ angle_restraints_z ]
 ; i    j    funct    phi    kc    n
6141    6142    1    0    100    1

So the angle between Z axis and two of them is zero with low force constant
- that will prevent protein from the rotation.

grompp with frozen dummies in all directions I got the error that DUM atoms
have a zero mass. Isnt it possible to have atoms with zero masses like
dummies? Shall I add a mass of 0.0000001 or would you suggest something
else? Maybe I should apply [ virtual_sites ] option?

Steven

On Tue, Jun 3, 2014 at 8:25 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 6/2/14, 9:43 PM, Steven Neumann wrote:
>
>> Thanks but it will take some time to install 5.0 on the cluster. How about
>> [ angle_restraints_z ]? I could think of an atom in the protein to
>> restrain
>> along z axis (protein length). Not sure how can I measure such an angle
>> though and which atom to choose.
>>
>>
> Possibly, but I've never tried using anything like that.  The flat-bottom
> potential is effectively the same as reflective boundary conditions that
> nearly all simulation software has used for a very long time.  No need to
> reinvent the wheel.
>
> As an aside, you can always install custom software within your own $HOME
> directory, unless the cluster has some weird rules about not running things
> from $HOME.  No need to bug a sysadmin, in most cases :)
>
> -Justin
>
>
>
>>
>> On Tue, Jun 3, 2014 at 9:21 AM, Justin Lemkul <jalemkul at vt.edu> wrote:
>>
>>
>>>
>>> On 6/2/14, 9:15 PM, Steven Neumann wrote:
>>>
>>>  On Mon, Jun 2, 2014 at 8:06 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>>>>
>>>>
>>>>
>>>>> On 6/2/14, 7:10 AM, Steven Neumann wrote:
>>>>>
>>>>>   Dear Users,
>>>>>
>>>>>>
>>>>>> I am trying to prevent rotation of my protein in recatngular box and I
>>>>>> am
>>>>>> thinking about applying some position restraints with the dummy
>>>>>> atoms. I
>>>>>> read some posts about this subject from 2003, 2006 but nothing recent.
>>>>>> Is
>>>>>>
>>>>>>
>>>>>>  Rather than risk wasting time by repeating things, if you're looking
>>>>> up
>>>>> information in old posts, please provide the links to those posts for
>>>>> context.
>>>>>
>>>>>
>>>>
>>>>
>>>> https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-
>>>> users/2006-July/022914.html
>>>>
>>>>
>>>>
>>>>>    there a gromacs tool to create a dummy atom a apply position
>>>>> restraints or
>>>>>
>>>>>  maybe a pull_code would be a solution? Please, provide me with some
>>>>>> information.
>>>>>>
>>>>>>
>>>>>>   You can restrain whatever you like, and I don't necessarily see the
>>>>>>
>>>>> need
>>>>> for a dummy atom in this case, but the larger question is - why do you
>>>>> need
>>>>> to prevent rotation?
>>>>>
>>>>> -Justin
>>>>>
>>>>>
>>>>>
>>>> I am studying protein in water. In the dodecahedron box I would have 80K
>>>> water molecules which on my GPU machine give 6 ns/day. If I place my
>>>> protein to the triclinic box I would get 20K atoms getting 50 ns/day.
>>>> Thats
>>>> a significant improvement. My protein in 15 nm long and 4 nm width so it
>>>> is
>>>> likely it can rotate and interact with its periodic image. I wish to
>>>> prevent the rotational movements. Would you suggest something?
>>>>
>>>>
>>>>  A flat-bottom restraint would probably accomplish the same thing,
>>> applying
>>> a restraint in the dimensions perpendicular to the long axis.  The
>>> flat-bottom potential is supported as of the first beta release of 5.0.
>>>
>>> -Justin
>>>
>>>
>>> --
>>> ==================================================
>>>
>>> Justin A. Lemkul, Ph.D.
>>> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>>>
>>> Department of Pharmaceutical Sciences
>>> School of Pharmacy
>>> Health Sciences Facility II, Room 601
>>> 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 601
> 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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> Gromacs Users mailing list
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