[gmx-users] Question of constraining bonds

Dong Woo Kang dongwoo0701 at kaist.ac.kr
Wed May 29 12:44:02 CEST 2019

Dear all gromacs users,I'm new to gromacs, and I have some questions about bond constraints.Now I have a system with methane, hydrogen, and TIP4P/Ew water. In special, topology of hydrogen molecule is including [ constraints ], for constructing a virtual site in the center of hydrogen molecule.By including "constraint-algorithm = lincs" and "constraints = h-bonds", I found that all bonds including H were constrained.So I changed *.mdp file with "constraint-algorithm = lincs" and "constraints = none", and I found that LINCS are applied to hydrogen, but it seemed that SETTLE is applied to water instead of LINCS.If I want to apply LINCS both on hydrogen molecules and waters, and not on methane or other hydrocarbons including hydrogen atoms, how can I do that?Any advices will be very helpful.Dong Woo Kang

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