[gmx-users] Membrane simulations

Smith, Micholas D. smithmd at ornl.gov
Tue Oct 21 14:25:07 CEST 2014

With a time step of 0.0005 and still having the "particle moved too far" error, I would suspect that your system is not well equilibrated. Likely you are going to need to do some energy minimization and a short simulation with position restraints to relax the system into equilibrium before doing your production study.

Micholas Dean Smith, PhD.
Post-doctoral Research Associate
University of Tennessee/Oak Ridge National Laboratory
Center for Molecular Biophysics
From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of lloyd riggs <lloyd.riggs at gmx.ch>
Sent: Monday, October 20, 2014 11:40 PM
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] Membrane simulations

Dear All,

So I have been doing membrane simulations on a small (really small) node for a few months, and was able to get in a few hundred nanoseconds of time.  I now have added 4 inositol lipids, and repeatedly encounter some errors as follows.

I set the time in the eq for 0.0005 and it runs about 25000 steps.  I then move up to a normal sim at 0.002 and it runs about 25000 steps then crashes with a particle moved to far error.  On inspection, these vary each time, but are always a membrane lipid /cholesterol or inositol atom, usually trying to move ithrough a periodic boundary temporarily?  I then run the sim again (continuation) for 25000 steps at 0.0005 again then it crashes again with the same eror.  I then Switch back to 0.002 as a continuation, and the same.  I have done this for around 10 ns now?  I woundered if there were any suggestions, as it makes it impossible to run a simulation unless you baby sit it constantly, and precludes submitting it to a server?  Please excusse my spelling.

Stephan Watkins, PhD

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