[gmx-users] Problem with equilibrated lipid bilayer structure

Jernej Zidar jernej.zidar at gmail.com
Mon Oct 15 09:10:18 CEST 2012

The reason for using SPCE instead of TIP3P is that it performs  way
better than TIP3P. This point is being emphasized everywhere along the
documentation. I will try simulating using TIP3P model.
> Is there a reason to switch water models? Gromacs supports both the
> traditional TIP3P and the CHARMM TIP3P (TIPS3P).
> Since you need to reinitialize velocities, it may not be a good idea to use
> Nose-Hoover and Parinello-Rahman straight away. Furthermore, you need
> to gen_vel=yes since gromacs has no velocity from your previous charmm run
> and subjecting an otherwise frozen system to a parinello-rahman thermostat is
> asking for trouble.

gen_vel=yes does not seem to help

> Also, pressure coupling for NPT should probably be semiisotropic for bilayers.
> Finally you may want to experiment with EnerPres; see also
> http://pubs.acs.org/doi/abs/10.1021/ct3003157 (although this isn't related to
> your crash).

EnerPres is already set.

  I tried your suggestions but the simulation still fails.

Jernej Zidar

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