[gmx-users] Bond lengths

suniba shuaib suniba88chemistry at gmail.com
Wed Jan 4 08:28:08 CET 2017

Dear Users
I have performed a 200 ns MD simulation of a protein and a small molecule
inhibitor of 30 atoms, using GROMOS 43a1 ff and Gromacs v 5.0. Taking
reference from a number of papers and similar systems, I have used LINCS
algorithm to constrain all bond lengths.
I have reported interactions like pi-pi and hydrogen bonding between
protein and ligand plus some other analysis and  recently i submitted my
article. Reviewers have asked few question one of which is:

*Q: Why you have constrained all bond lengths? A good force field should
permit free variation of the bond lengths and only high frequency motions
(C-H) should be constrained.*

As i visited mailing list, I found an answer by Justin Lemkul:

*"The effects of H-bond vibrations aren't of interest for the problems
at hand; if you want to model bond formation, you can't accept a model
that has no "electron vibrations," and *that* drives your choice of
time step."*

Another reply by Mark Abraham:
"*Force field parameters are (unfortunately) co-optimized with and
dependent on*

*implementation issues like size of time step and lengths of cut-offs. The
use of constraints=all-bonds couples constraints across a whole polymer; if
that's a protein simulated using a spatial domain decomposition, those
atoms are widely distributed on the machine and the communication required
for the iterative constraint solver can become rate limiting at extreme
scale. Reducing the constraint iteration to a single node is unattractive
if the rest of the machine lies idle - which is part of why we'd like to
improve the ability to deploy task parallelism in GROMACS at scale. The
main alternative is using shorter time steps (maybe no constraints at all!)
- if they only way you can get 10x greater sampling rate for a single
simulation is by using 100x the hardware at one tenth of the time step,
then that could be a serious option.

I think that feeling that "constrained H bonds" is natural and "constrained
heavy-atom bonds" is artificial is wrongly conflating experience with

After reading these answers, I am little confused how should i respond
to the raised question. In my case, I believe, it was not necessary to
keep the system unconstrained. Plus, from Mark's answer, I concluded
that it is better to keep all bonds constrained? Please clear my

Thank You


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