[gmx-users] Distance restraint and pull code

[Justin Lemkul]

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

==================================================