[gmx-users] Running free energy tutorial for ionic molecules

[vivek sharma]

Hi users and experts,

I am trying to run a free energy tutorial by Dr Lemkul provided at:
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/free_energy/
My system is an ionic pyridinium molecule unlike the methane molecvule used
in the tutorial, following are the steps I am following for my runs:
1. I downloaded the molecule structure and topology from ATB site:
http://compbio.biosci.uq.edu.au/atb/index.py?tab=existing_tab&nocache=153
2. I set up the system using octanol water box.
3. I am using the MDP parameters as suggested in the advanced application
section: decoupling vdw and coulombic interaction step by step.
4. WHile running the simulation it goes fine till npt equilibration step,
but it fails during the production run with the LINCS warnings, like some
angles are rotating more than 30 degree.

I am unable to figure out if I can apply this protocol on ionic molecules
or I am doing something wrong in setting up the system.

Can somebody help me in understanding the possible reason for error?

It will be really helpful to get more insights into this type of simulation.

Thanks and regards,
Vivek