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” ?
There is a short discussion on constraints in Gromacs manual chapter 1.2 highlighting the difference between quantum and classical harmonic oscillators - somenthing what should be kept in mind.
Personally, I think you don't need oscillating bonds by default. Constraint is a sort of coarse-graining or decreasing of dimensionality of your problem, which can be beneficial. Further, I would say that all-bonds constraints are typically used in the community to reach larger than 2 fs integration step.
Where did you see such thing? This is not a general rule and just a trick to increase the time step (as you said) when detail of bonds' oscillation is not important. Usually for complex system constraining all bonds make simulation slower (handling constraint is more expensive than normally integrating them by MD). Also simulation is prone to failure at high temperatures.
There is a short discussion on constraints in Gromacs manual chapter 1.2 highlighting the difference between quantum and classical harmonic oscillators - somenthing what should be kept in mind.
Personally, I think you don't need oscillating bonds by default. Constraint is a sort of coarse-graining or decreasing of dimensionality of your problem, which can be beneficial. Further, I would say that all-bonds constraints are typically used in the community to reach larger than 2 fs integration step.
Dear Mr. Garcia,
I think your referred mdp file is :
http://md.chem.rug.nl/~mdcourse/md.mdp
you are right about constraint parameter which is set to all- bonds but you should considered next line of mdp file(unconstrained_start= yes). I suggest reading gromacs manual before proceeding.
hope it helps.
HHA
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