[gmx-users] Problem with equilibrated lipid bilayer structure
Peter C. Lai
pcl at uab.edu
Mon Oct 15 09:17:01 CEST 2012
On 2012-10-15 03:10:18PM +0800, Jernej Zidar wrote:
> 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
Have you tried just doing NVT with tcoupl = V-rescale and tau_t = 0.1 0.1?
> > 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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Peter C. Lai | University of Alabama-Birmingham
Programmer/Analyst | KAUL 752A
Genetics, Div. of Research | 705 South 20th Street
pcl at uab.edu | Birmingham AL 35294-4461
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