[gmx-users] pressure coupling for lipid bilayer

[David van der Spoel]

On Wed, 1 May 2002, David L. Bostick wrote:

>I use anisotropic with
>
>compressibility         = 4.5e-5 4.5e-5 4.5e-5 0.0 0.0 0.0
>
>It seems to work quite well.  Since the 0.0 compressibilities of the
>off-diagonal elements keep the box from deforming.
And use large tau_p, since you don't have the averaging effect of
isotropic scaling. I suggest to use at least 5 ps.

>David
>
>-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=
>David Bostick					Office: 262 Venable Hall
>Dept. of Physics and Astronomy			Phone:  (919)962-0165 
>Program in Molecular and Cellular Biophysics 
>UNC-Chapel Hill					
>CB #3255 Phillips Hall				dbostick at physics.unc.edu	
>Chapel Hill, NC 27599	           		http://www.unc.edu/~dbostick	
>=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-
>
>On Wed, 1 May 2002, Shang-Te Danny Hsu wrote:
>
>> Hi!
>> 
>> There has been some discussions about proper pressure coupling for lipid 
>> bilayer. My experience is that the anisotropic or semiisotropic coupling 
>> with compressibility of 6e-5 or 4.5e-5 along the membrane normal easily 
>> deforms the bilayer in < 20ps and eventually the bilayer is flattened!! 
>> On the other hand, with isotropic or without any P-coupling, the system 
>> is running quite well.
>> 
>> Surface tension coupling method is suggested to be a nice approach (J. 
>> Chem. Phys. 111(3):1281), but the parameters are not trivial. Without 
>> experimental data on hand, it is difficult to estimate surface tension 
>> (in my case, POPC bilayer). In addition, the incorporation of other 
>> molecules may alter the surface tension again!
>> 
>> How should I setup up such a system properly???
>> -- 
>> Shang-Te Danny HSU
>> Department of NMR Spectroscopy
>> Bijvoet Center for Biomolecular Research
>> Utrecht University
>> Padualaan 8, 3584 CH Utrecht, the Netherlands
>> phone: +31-30-2539931 | fax: +31-30-2537623
>> e-mail: hsu at nmr.chem.uu.nl
>> 
>> _______________________________________________
>> 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.
>> 
>
>_______________________________________________
>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.
>

Groeten, David.
________________________________________________________________________
Dr. David van der Spoel, 	Biomedical center, Dept. of Biochemistry
Husargatan 3, Box 576,  	75123 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://zorn.bmc.uu.se/~spoel
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++