# LINCS constraints all bonds to h-bonds only **URL:** \ **Category:** pmx\ **Created:** [February 16, 2024, 9:31am UTC](https://ask.bioexcel.eu/t/lincs-constraints-all-bonds-to-h-bonds-only/4839 "2024-02-16T09:31:53Z")\ **Posts on this page:** 8\ **Page:** 1
**Author:** ![obeyens](https://avatars.discourse-cdn.com/v4/letter/o/c77e96/32.png) [@obeyens](https://ask.bioexcel.eu/u/obeyens)\ **Post date:** [February 16, 2024, 9:31am UTC](https://ask.bioexcel.eu/t/lincs-constraints-all-bonds-to-h-bonds-only/4839/1 "2024-02-16T09:31:53Z")
Hi everyone, In the mdp files on the github pages of pmx benchmarks, LINCS constraints are always set to ‘all-bonds’. However, this causes a significant hit in performance on GPUs as the -update gpu flag to mdrun cannot be used. I think that in the Amber99SB-ILDN paper, constraints are also set to h-bonds only. Is there a specific reason as to why LINCS constraints are always set to ‘all-bonds’ in pmx? Is it “safe” in terms of accuracy to set the constraints to h-bonds for simulations done with the Amber force field only? Kind regards, Olivier ---
**Author:** ![bgroot](https://avatars.discourse-cdn.com/v4/letter/b/dc4da7/32.png) [@bgroot](https://ask.bioexcel.eu/u/bgroot)\ **Post date:** [February 16, 2024, 10:11am UTC](https://ask.bioexcel.eu/t/lincs-constraints-all-bonds-to-h-bonds-only/4839/2 "2024-02-16T10:11:22Z")
setting constraints to h-bonds should be safe in this case as long as you limit the time step to 2 fs or less ---
**Author:** ![obeyens](https://avatars.discourse-cdn.com/v4/letter/o/c77e96/32.png) [@obeyens](https://ask.bioexcel.eu/u/obeyens)\ **Post date:** [February 16, 2024, 10:12am UTC](https://ask.bioexcel.eu/t/lincs-constraints-all-bonds-to-h-bonds-only/4839/3 "2024-02-16T10:12:36Z")
Great, thanks! ---
**Author:** ![vgapsys](https://avatars.discourse-cdn.com/v4/letter/v/7993a0/32.png) [@vgapsys](https://ask.bioexcel.eu/u/vgapsys)\ **Post date:** [February 16, 2024, 10:25am UTC](https://ask.bioexcel.eu/t/lincs-constraints-all-bonds-to-h-bonds-only/4839/4 "2024-02-16T10:25:09Z")
Also, make sure to use ‘develop’ branch of pmx and do not allow for hydrogen-to-heavy\_atoms morphs. ---
**Author:** ![obeyens](https://avatars.discourse-cdn.com/v4/letter/o/c77e96/32.png) [@obeyens](https://ask.bioexcel.eu/u/obeyens)\ **Post date:** [February 16, 2024, 10:58am UTC](https://ask.bioexcel.eu/t/lincs-constraints-all-bonds-to-h-bonds-only/4839/5 "2024-02-16T10:58:40Z")
I can understand why hydrogen-to-heavy\_atoms morphs are not allowed, but why is it necessary to use the develop branch? ---
**Author:** ![vgapsys](https://avatars.discourse-cdn.com/v4/letter/v/7993a0/32.png) [@vgapsys](https://ask.bioexcel.eu/u/vgapsys)\ **Post date:** [February 16, 2024, 2:01pm UTC](https://ask.bioexcel.eu/t/lincs-constraints-all-bonds-to-h-bonds-only/4839/6 "2024-02-16T14:01:48Z")
It is the branch with the latest updates ---
**Author:** ![obeyens](https://avatars.discourse-cdn.com/v4/letter/o/c77e96/32.png) [@obeyens](https://ask.bioexcel.eu/u/obeyens)\ **Post date:** [February 16, 2024, 2:05pm UTC](https://ask.bioexcel.eu/t/lincs-constraints-all-bonds-to-h-bonds-only/4839/7 "2024-02-16T14:05:20Z")
Are there any specific reasons as to why the master branch will not work? Also, is it now recommended to use the develop branch, as the github page still mentions it is not a stable/reliable release? ---
**Author:** ![vgapsys](https://avatars.discourse-cdn.com/v4/letter/v/7993a0/32.png) [@vgapsys](https://ask.bioexcel.eu/u/vgapsys)\ **Post date:** [February 16, 2024, 2:43pm UTC](https://ask.bioexcel.eu/t/lincs-constraints-all-bonds-to-h-bonds-only/4839/8 "2024-02-16T14:43:58Z")
Amino acid mutation libraries in the ‘master’ branch allow hydrogen to heavy atom transformations, therefore LINCS has to be set to all-bonds.