[gmx-users] Distance restraint and pull code

[Hong Tham]

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
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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