[gmx-users] Distance restraint and pull code

[Justin Lemkul]

On 6/9/16 11:21 AM, Hong Tham wrote:
> hi Justin,
> in the manual, the [distance restraint] will add flat-bottom harmonic potential to keep distance between 2 atoms. The low, up1, up2 is corresponds to ro, r1, r2 in the equation 4.83 (manual 5.0.7).
> I understand if rij < r low,   up1 <rij > up2, mdrun will add the harmonic potential, if rij > up2 , the linear potential will be added. no potential is added if low < rij < r up1.
> However, because the pull code will add harmonic potential, I did think the distance restraint should do the same thing ( harmonic restraint instead of flat-bottom harmonic restraint). I am compare between 2 way in maintaining the zn coordination. Therefore, I did set the r low = r up1, r up 2 very big. I intend to let mdrun recognize if rij < r low = r up1 or rij > r up2, the harmonic potential will be added. I expect that the distance rij between 2 atoms can not reach that high r up2. and I think, after modifying, the 4.83 equation will look like 4.31 (harmonic potential).
> even, if i run genrestr to generate the distance restraint itp which is later included in the topology file, it return the [distance restraint] with low = up1, the disre-up2 is the up2 value.
> As your reply, that mean I can not do like that? Gromacs can not recognize that, and it will do the way as you mentioned? I don’t want that, actually. So, If I want to apply distance restraint, just simply use flat-bottom potential?
> Sorry if I did ask like that, I’m still studying to understand more about Gromacs and how it works. and sometime, I may misunderstand. :D

If you want a plain harmonic potential between different atoms, use bond type 6 
(does not generate exclusions, not subject to constraints).

-Justin

> Thanks so much ^^
> HT
>
>
>> On Jun 9, 2016, at 9:58 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>>
>>
>>
>> On 6/9/16 8:54 AM, HongTham wrote:
>>> 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.
>>
>> Your distance restraints make no sense.  Look at figure 4.15 in the manual. You're telling mdrun "apply zero biasing potential from 0.21 - 5.21 (or 0.4 - 5.4) nm), then try to make the potential steeper from 5.21 - 4 nm (or 5.4 - 2 nm).  So mdrun does what you tell it; essentially no restraint is applied unless the distances are massive.
>>
>> -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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>

-- 
==================================================

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

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