[gmx-users] loiuc vermeer-seperating bilayers.

Erik Lindahl lindahl at sbc.su.se
Fri Sep 9 19:24:26 CEST 2005

Hi Rama,

Great that it worked.

For reference - the relaxation time for individual lipid  
reorientation is in the order of 5-10 nanoseconds. In comparison,  
water molecules reorient on picosecond scale, so it's not surprising  
that you must use a much weaker coupling for bilayers.



On Sep 9, 2005, at 6:34 PM, Ramachandra Rao Gullapalli wrote:

> Dear Louic,
> I had this problem a couple of weeks ago and when i posted the  
> questions erik
> kindly replied back. However, the one thing that did work for me  
> was that i ran
> an NPT simulation with an increased tau_p. Earlier i was using a  
> tau_p of 0.5,
> but when i increased it to 5.0, the seperation dissappeared, albeit
> magically..:-)
>  Also one thing that i think helps is to run the simulation  
> intially with NVT
> ensemble and then switch to NPT with the above mentioned  
> parameters. However, i
> m beginning to understand the importance of properly equilibriating  
> a bilayer
> for long times before using it for actually running it.
> I dont know if it helps, but let me know.
> Sincerely
> Regards
> Rama
> The important thing is not to stop questioning. Curiosity has its  
> own reason for existing...
> -Einstein
> _______________________________________________
> gmx-users mailing list
> gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.

More information about the gromacs.org_gmx-users mailing list