GROMACS version:2023
GROMACS modification: Yes/No
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Hi everyone,
I need to solvate a system with non-water, which i have gro file, do i need to remove the solvent.gro box information? i found that when i remove the box inforamtion it adds more number of sovlent molecule for a a particular box.
Hi alexmathew,
What do you mean by ‘box information’? You mean the box dimensions (last line)?
What has worked consistently for me is to give a box that has been equilibrated at the target temperature and pressure to -cs. I believe that if you start from a single molecule (which may be your case?), gmx solvate doesn’t really work, since it tries to tile the input box. That may also explain why changing the box dimensions tunes the amount of solvent molecules.