[gmx-users] Distance restraint and pull code

[HongTham]

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?
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 ;

Thank you so much,

Hongtham

On Sat, May 28, 2016 at 12:10 AM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 5/26/16 9:20 PM, HongTham wrote:
>
>> Dear Gromacs users,
>> Im running a Zn bound protein -  ligand complex system. Zn makes
>> coordinations with 3 HIS and NH- of ligand. in the itp file, Zn and
>> protein
>> in the same [molecule] but not ligand. because it cant be applied distance
>> restraint ZN and ligand (they are belong to different [molecule]), I
>> applied distance restraint for ZN and 3 HIS, and used pull code to keep
>> ligand closed to ZN
>> This is the distance restrains assigment in topology file of ZN and
>> protein, while 3852 is ZN and other is HIS atoms.
>> [ distance_restraints ]
>> ; ai   aj   type index type   low up1 up2 fac
>>   3852 1354  1    0     1     0.2 0.21 0.22 0.1
>>   3852 1390  1    0     1     0.2 0.21 0.22 0.1
>>   3852 1721  1    0     1     0.2 0.21 0.22 0.1
>>
>> The pull code in mdp file is like below, in which, a_3862 is N atom of
>> ligand
>> disre       = simple ; distance restraints
>> disre_fc    = 1000   ; Force constant
>> pull = umbrella
>> pull-ngroups = 2
>> pull-ncoords = 1
>> pull-group1-name = ZN
>> pull-group2-name = a_3862
>> pull-geometry = distance ; simple distance increase
>> pull-coord1-groups = 1 2
>> pull-dim = Y Y Y
>> pull-coord1-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-start = yes ; define initial COM distance > 0
>> pull-nstxout     = 5000
>> pull-nstfout     = 5000
>>
>>
>> It seemed the pull code worked well. The problem is the distance restraint
>> is not effective. ZN only can be kept closed to one of three HIS, and
>> moves
>> far away from 2 others.
>>
>
> Because you defined one restraint using the pull code.  Either define
> multiple restraints or increase the strength of your distance restraints.
>
> -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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