[gmx-users] all-bonds constraints

[Juan Munoz-Garcia]

Dear GROMACS users,

I’m quite new with GROMACS. I come from using AMBER for a long time and after doing quite a few GROMACS tutorials I’ve found in all of them that the variable “constraints" is set to “all-bonds” even during the production run. I’m quite surprised about this. My understanding as I learnt from AMBER is that due to the high frequency of motion of the bonds with H atoms (aprox 1 fs timescale) those are fixed during the integration time step as this is longer (usually 2 fs) than the motion frequency. However, all other bonds are not fixed because their motions have larger timescales (of course this is a simplification) than the integration time step. I find that constraining all bonds is too “artificial” as the  bond length is supposed to be oscillating between the equilibrium values given by the force field. As this is a quite important difference compared to what I was used to in AMBER, I’d like you to please tell me why is it “constraints = all-bonds” generally used during the production run instead of “constraints = h-bonds” ?

Thank you.

Juan C. Munoz-Garcia, PhD
Biomembrane Structure Unit
University of Oxford	
South Parks Road
Oxford OX1 3QU
juan.munoz-garcia at bioch.ox.ac.uk