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

[vivek sharma]

Dear Users,
I am resending this mail, as I am still stuck with the error. Now I have
upgraded my Gromacs from version-4.5.5. to version-5.0.2, I am able to run
the simulation using Gromacs-5.0.2 for sytems with 1-octanol as solvent,
whereas the system with water as solvent is still giving errors with LINCS
warnings.
I assume if the runs are going fine with water system then my topology and
MDP (adapted from tutorial) files are in place, Please correct me if this
is a wrong assumption.
It will be really helpfull if anybody can help me in understanding the
system behaviour or possible reasons for the error.


regards,
Vivek

---------- Forwarded message ----------
From: vivek sharma <viveksharma.iitb at gmail.com>
Date: 10 October 2014 09:01
Subject: Running free energy tutorial for ionic molecules
To: Discussion list for GROMACS users <gmx-users at gromacs.org>


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