# Relative constraint deviation after LINCS
**URL:** https://ask.bioexcel.eu/t/relative-constraint-deviation-after-lincs/2496
**Category:** pmx
**Created:** [October 5, 2020, 10:54pm UTC](https://ask.bioexcel.eu/t/relative-constraint-deviation-after-lincs/2496 "2020-10-05T22:54:45Z")
**Posts on this page:** 16
**Page:** 1
### Author:  [@dburns](https://ask.bioexcel.eu/u/dburns)
#### Post date: [October 5, 2020, 10:54pm UTC](https://ask.bioexcel.eu/t/relative-constraint-deviation-after-lincs/2496/1 "2020-10-05T22:54:45Z")
Hello,
I’m using the eqA.mdp file from the tutorial here:
> **[Ligand modification free energy calculations](http://pmx.mpibpc.mpg.de/summerSchool2020_tutorial2/index.html)**
Despite running several equilibration steps with and without restraints on my ligand I get the error:
Step 3, time 0.006 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.001067, max 0.057983 (between atoms 9731 and 9732)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
I can see the dummy atoms swinging around like crazy when I visualize the equilibration trajectory. I don’t know why the equilibration doesn’t crash but the run started from the provided mdp file does.
Apparently an mdp setting I need to adjust?
Or is it an issue with my ligand structure? I can’t see why this would be the case since this is a structure I’ve used in many simulations (without the dummy atoms).
Thank you,
Dan
---
### Author:  [@dburns](https://ask.bioexcel.eu/u/dburns)
#### Post date: [October 5, 2020, 11:33pm UTC](https://ask.bioexcel.eu/t/relative-constraint-deviation-after-lincs/2496/2 "2020-10-05T23:33:20Z")
I switched the constraints from “all-bonds” to “h-bonds” and it eliminated the errors.
---
### Author:  [@vgapsys](https://ask.bioexcel.eu/u/vgapsys)
#### Post date: [October 9, 2020, 3:32pm UTC](https://ask.bioexcel.eu/t/relative-constraint-deviation-after-lincs/2496/3 "2020-10-09T15:32:16Z")
Switching to h-bond constraints is likely incorrect for the pmx based ligand hybrid topologies. In case, a hydrogen atom is mapped to a dummy in stateA, the constraint will not be generated for the bonds involving this dummy.
I would suggest trying an SD integrator (note that you need to change tau-t in this case).
---
### Author:  [@dburns](https://ask.bioexcel.eu/u/dburns)
#### Post date: [October 9, 2020, 3:50pm UTC](https://ask.bioexcel.eu/t/relative-constraint-deviation-after-lincs/2496/4 "2020-10-09T15:50:27Z")
Okay, thank you. In the case of an SD integrator, I would return constraints = all-bonds?
Thanks, Vytas.
Dan
---
### Author:  [@vgapsys](https://ask.bioexcel.eu/u/vgapsys)
#### Post date: [October 9, 2020, 4:12pm UTC](https://ask.bioexcel.eu/t/relative-constraint-deviation-after-lincs/2496/5 "2020-10-09T16:12:22Z")
Yes. It is not guaranteed that the SD integrator will help, as there might be other issues, but it is worth to try it out.
Is this simulation started right after energy minimization? If so, what is the maximal force at the end of the EM?
---
### Author:  [@dburns](https://ask.bioexcel.eu/u/dburns)
#### Post date: [October 9, 2020, 4:17pm UTC](https://ask.bioexcel.eu/t/relative-constraint-deviation-after-lincs/2496/6 "2020-10-09T16:17:30Z")
The first time around I ran nvt and npt equilibration.
This time I went straight from em to the included eq mdp. The maximum force was 2.203x10^3.
Could I go from the eq run with md integrator and my h-bond constraint to the TI runs with the sd integrator all-bond constraint without issue?
---
### Author:  [@vgapsys](https://ask.bioexcel.eu/u/vgapsys)
#### Post date: [October 9, 2020, 4:31pm UTC](https://ask.bioexcel.eu/t/relative-constraint-deviation-after-lincs/2496/7 "2020-10-09T16:31:39Z")
I would recommend to retain consistent use of constraints and integrator for both steps: eq and transitions.
---
### Author:  [@s.pallav](https://ask.bioexcel.eu/u/s.pallav)
#### Post date: [December 6, 2024, 5:57am UTC](https://ask.bioexcel.eu/t/relative-constraint-deviation-after-lincs/2496/8 "2024-12-06T05:57:23Z")
Encountering similar error(Relative constraint deviation after LINCS) at the last lambda window( at lambda=1) and is for the atoms which are transformed to dummy. I have been using h-bond constraints and not all-bond constraints cause it does not involve any hydrogen to heavy atom morphing. Would using SD integrator alleviate the issue? Or it has to do with free energy settings (note that it is a K2A transformation)?
---
### Author:  [@vgapsys](https://ask.bioexcel.eu/u/vgapsys)
#### Post date: [December 7, 2024, 11:24am UTC](https://ask.bioexcel.eu/t/relative-constraint-deviation-after-lincs/2496/9 "2024-12-07T11:24:15Z")
could it be that you are using ‘master’ branch of pmx? In that case, you need to use all-bond constraints. h-bond constraints are supported on with the ‘develop’ branch
---
### Author:  [@s.pallav](https://ask.bioexcel.eu/u/s.pallav)
#### Post date: [December 9, 2024, 5:17am UTC](https://ask.bioexcel.eu/t/relative-constraint-deviation-after-lincs/2496/10 "2024-12-09T05:17:26Z")
I am using the develop branch. I am attaching the topology for the same. Using all-bonds must solve the problem cause the dummy atoms are causing the problem. Is there any other issue which might have been causing it?
```auto
~/Softwares/pmx$ git branch
* develop
master
```
---
### Author:  [@s.pallav](https://ask.bioexcel.eu/u/s.pallav)
#### Post date: [December 9, 2024, 6:04am UTC](https://ask.bioexcel.eu/t/relative-constraint-deviation-after-lincs/2496/11 "2024-12-09T06:04:38Z")
Compared the same with tripeptide data as provided in the website, it is the same topology.
---
### Author:  [@vgapsys](https://ask.bioexcel.eu/u/vgapsys)
#### Post date: [December 9, 2024, 7:59am UTC](https://ask.bioexcel.eu/t/relative-constraint-deviation-after-lincs/2496/12 "2024-12-09T07:59:13Z")
Webserver is still using ‘master’ branch, this means that you are likely also using ‘master’ branch, thus you need to use all-bond constraints. Maybe your GMXLIB is still pointing to the force field folder in the ‘master’ branch? For h-bond constraints, switch to ‘develop’ branch. Make sure to use amber99sb-star-ildn-mut.ff, amber14sbmut.ff or charmm36m-mut.ff force field.
---
### Author:  [@s.pallav](https://ask.bioexcel.eu/u/s.pallav)
#### Post date: [December 9, 2024, 9:25am UTC](https://ask.bioexcel.eu/t/relative-constraint-deviation-after-lincs/2496/13 "2024-12-09T09:25:00Z")
> [@vgapsys](#):
>
> Maybe your GMXLIB is still pointing to the force field folder in the ‘master’ branch?
yes, got that. This was the reason for the problem. Thanks a lot.
---
### Author:  [@s.pallav](https://ask.bioexcel.eu/u/s.pallav)
#### Post date: [December 9, 2024, 9:50am UTC](https://ask.bioexcel.eu/t/relative-constraint-deviation-after-lincs/2496/14 "2024-12-09T09:50:05Z")
Would it differ in deldelG values with the use of different constraints
---
### Author:  [@vgapsys](https://ask.bioexcel.eu/u/vgapsys)
#### Post date: [December 9, 2024, 11:10am UTC](https://ask.bioexcel.eu/t/relative-constraint-deviation-after-lincs/2496/15 "2024-12-09T11:10:49Z")
Both legs of the thermodynamic cycle need to use the same simulation parameters, i.e. the same constraints
---
### Author:  [@s.pallav](https://ask.bioexcel.eu/u/s.pallav)
#### Post date: [December 9, 2024, 11:13am UTC](https://ask.bioexcel.eu/t/relative-constraint-deviation-after-lincs/2496/16 "2024-12-09T11:13:56Z")
Certainly, thanks.