[gmx-users] Distance restraint and pull code

[Justin Lemkul]

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

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