Energy minimization

User discussions
1

GROMACS version: 2018.3
GROMACS modification: No

I want to know is it necessary to use LINCS constraints in EM step for simulation of small molecules? I tried some tutorials but can’t find any conclusion as sometimes it is used and sometimes not.

Thanks in advance for your help.
Dhrubajyoti Maji

2

Hello,

you would typically run your energy minimization with the same constraints as your production simulation. So if you are using LINCS later, use it for the EM step too.

Regards,
Petter

3

Many thanks Petter. A little confusion here. In many tutorials like the ‘Lysozyme in water’, no bond-constraint parameter is specified in EM mdp file. So I wonder if it is optional or necessary ? Looking forward for your valuable input.

Thanks again,
Dhrubajyoti