[gmx-users] Distance restraint and pull code

Thu Jun 9 14:55:20 CEST 2016

Hi,
I have another question. I applied 4 pull codes (3 to keep Zn ion in
coordination with 3 HIS, 1 to keep Zn ion in coordination with the ligand).
The pull code worked effectively.
With the same system, when applying 3 distance restraints (to keep Zn ion
in coordination with 3 HIS) and 1 pull code to keep the Zn ion in
coordination with the ligand. However, the distance restraints didn't work.
The distance restraints and pull code for restrains in principle both work
in the same manner. In both cases,  a harmonic potential is added to
maintain the distance between 2 selections.
However, there is an inconsistency between the two approaches.
This is the distance restaints code:
[ distance_restraints ]
;   i     j       type  label      funct    lo        up1        up2
weight
 1354  3852 1     1         1   0.21       0.21    5.21             4
 1390  3852 1     2         1   0.21       0.21    5.21             4
 1721  3852 1     3         1   0.21       0.21    5.21             4
 1520  3852 1     4         1   0.40       0.40    5.40             2

which is included in the topology file.

The pull codes used are similar to the previous, only changed the
pull-coord-k parameter(s) to be the same with the distance restraints.
pull-coord1-k = 4000 ; kJ mol^-1 nm^-2
pull-coord2-k = 4000 ; kJ mol^-1 nm^-2
pull-coord3-k = 4000 ; kJ mol^-1 nm^-2
pull-coord4-k = 2000 ; kJ mol^-1 nm^-2

The question is, why is there an inconsistency? The distance between the
histidines and the Zn ion keeps increasing as the simulation is
progressing, if distance restraints are applied. If only pull codes are
used, then everything is fine. All the distances converge well.
Thank you,
HT

On Fri, Jun 3, 2016 at 10:47 AM, HongTham <hongtham0709 at gmail.com> wrote:

> 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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