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

Dallas Warren Dallas.Warren at monash.edu
Thu Oct 16 02:05:59 CEST 2014

Which bonds are rotating too far?

At what lambda values and which decoupling process is this occurring?

Catch ya,

Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3052
dallas.warren at monash.edu
+61 3 9903 9304
When the only tool you own is a hammer, every problem begins to resemble a nail. 

> -----Original Message-----
> From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se
> [mailto:gromacs.org_gmx-users-bounces at maillist.sys.kth.se] On Behalf Of
> vivek sharma
> Sent: Wednesday, 15 October 2014 8:07 PM
> To: Discussion list for GROMACS users
> Subject: [gmx-users] Fwd: Running free energy tutorial for ionic
> molecules
> 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
> 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=1
> 53
> 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
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