Fix bond length

[nsigal]

GROMACS version: 5.1.5.
GROMACS modification: Yes/No
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I want to ask about fixing the bond length in Gromacs. Specifically, I want to use TraPPE for united atom polypropylene.
First of all, I read that I can fix the bonds in the mdp file by choosing “constraints=all-bonds” and “constraint-algorithm=LINCS”. Is that correct? Is something about LINCS parameters that I have to take into consideration?
Moreover, what should I write for bonded interactions in the top file? For example, should I choose a harmonic potential? Does it play a role?
Finally, is there a way to fix the bond length from the top file? One way I was thinking is to increase a lot the force constant in the harmonic equation of bonded interactions. Is that reasonable or will it have a totally different effect than the LINCS algorithm?
Any answer would be appreciated. Thank you in advance.

[jalemkul]

@nsigal

First of all, I read that I can fix the bonds in the mdp file by choosing “constraints=all-bonds” and “constraint-algorithm=LINCS”. Is that correct?

That is correct.

@nsigal

Moreover, what should I write for bonded interactions in the top file? For example, should I choose a harmonic potential? Does it play a role?

Bonded parameters are irrelevant when the bonds are constrained.

@nsigal

Finally, is there a way to fix the bond length from the top file?

You can explicitly define a constraint length in the topology simply by supplying the value. Normally these are read from the force field b₀ value.

@nsigal

One way I was thinking is to increase a lot the force constant in the harmonic equation of bonded interactions. Is that reasonable or will it have a totally different effect than the LINCS algorithm?

This will not fix the bond lengths, and will potentially break the assumptions of the force field.

[nsigal]

Thank you a lot for your answer. It is totally clear to me.