[gmx-users] Separate permeating water molecule from solvent water

Michail Palaiokostas Avramidis m.palaiokostas at qmul.ac.uk
Mon Feb 29 02:42:40 CET 2016

Dear GMX users,

I am trying to simulate water permeating through a lipid bilayer with CHARMM36. I am doing this by using the pull - constraint algorithm to constrain the distance of water and membrane to a specific depth.
I have noticed that the simulation crashes with LINCS warnings at a random time, even after 10s of nanoseconds, only when I simulate water and not other small molecules.

I have read in the GROMACS documentation that if a water molecule is separated from the rest of the solvent, this might create instabilities. So far I have been treating the water permeant as part of the solvent in the topology file and therefore, I am convninced that the mistake is there.

I would therefore like to ask how I can create a new water topology of CHARMM TIP3P just for the permeating water.

Shall I just copy the tip3p topology that is included in CHARMM36 folder in a new itp?

Thanks in advance.

Kind Regards,


Michail (Michalis) Palaiokostas
PhD Student
School of Engineering and Materials Science
Queen Mary University of London

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