[gmx-users] Distance restraint and pull code

[HongTham]

Hi Justin,
I got it.
Thank you for your explanation. :D
Hongtham

On Wed, Jun 1, 2016 at 7:38 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 6/1/16 5:16 AM, HongTham wrote:
>
>> Hi,
>> Im now applying 4 pull codes to keep the Zn coordination. the script is
>> like below.
>> ; Pull code
>> pull = umbrella
>> pull-ngroups = 5
>> pull-ncoords = 4
>> pull-group1-name = ZN
>> pull-group2-name = a_3862
>> pull-group3-name = a_1354
>> pull-group4-name = a_1390
>> pull-group5-name = a_1721
>> pull-geometry = distance ; simple distance increase
>> pull-coord1-groups = 1 2
>> pull-coord2-groups = 1 3
>> pull-coord3-groups = 1 4
>> pull-coord4-groups = 1 5
>> pull-dim = Y Y Y
>> pull-coord1-rate = -0.005 ; not pull, just distance restraint at a
>> reference distance bw 2 groups
>> pull-coord2-rate = 0.0 ; not pull, just distance restraint at a reference
>> distance bw 2 groups
>> pull-coord3-rate = 0.0 ; not pull, just distance restraint at a reference
>> distance bw 2 groups
>> pull-coord4-rate = 0.0 ; not pull, just distance restraint at a reference
>> distance bw 2 groups
>> pull-coord1-k = 1000 ; kJ mol^-1 nm^-2
>> pull-coord2-k = 1000 ; kJ mol^-1 nm^-2
>> pull-coord3-k = 1000 ; kJ mol^-1 nm^-2
>> pull-coord4-k = 1000 ; kJ mol^-1 nm^-2
>> pull-start = yes ; define initial COM distance > 0
>>
>> Because the ligand is quite big, so in the initial structure, the distance
>> between ZN and ligand is quite big (~ 0.5 nm). my target is to keep the
>> distance between Zn and other atom is about 0.2 nm. with The
>> pull-coord1-rate=-0.005 nm,  i want to quickly pull the ligand to come
>> close to Zn. and run NPT which protein backbone restrainted in 1 ns. after
>> NPT, now the distance between Zn and ligand is close enough, I will remove
>> the pull-rate in the md.mdp.
>> the question is, how can I keep the current ZN coordination in MD which a
>> specified distance?
>>
>
> A zero pull rate in conjunction with an appropriately specified restraint
> distance.
>
> I added one more option about the referece distance like below. is it right
>> for my intention? because the defaut value is 0.0 (at t=0), and I didnt
>> specity these value when I run NPT ( the above script), and I thought
>> Gromacs assigned the distance from the input structure as the reference
>> distance instead of 0. so I am really confused about this option.
>> pull-coord1-init= 0.21 ;
>> pull-coord2-init= 0.21 ;
>> pull-coord3-init= 0.21 ;
>> pull-coord4-init= 0.20 ;
>>
>>
> pull-start = yes means "use whatever the distances in the coordinate file
> are."
> pull-coord*-init = X means "use this value because I'm telling you to."
>
>
> -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
>
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