[gmx-users] Help to membranes pressure

[Andrey V. Golovin]

Dear Absalom.
I quite easily succeed with bilayer self-assembly using simple anisotropic
scheme and water compressibility on all major dimensions.

----
Best regards, Andrey
----------------------------------------------------------------
Andrey V. Golovin
Ph.D,Professor assistant    tel: +7 (095) 939-5305  
Bioengineering and
Bioinformatics Department              
Moscow State University     fax: +7 (095) 939-3181
119899 Moscow            E-mail: golovin at genebee.msu.su
Russia                      web: http://rnp-group.genebee.msu.su
-----------------------------------------------------------------


---------- Original Message -----------
From: Absalom Zamorano <absalomz2002 at yahoo.com.mx>
To: gmx-users at gromacs.org
Sent: Mon, 7 Mar 2005 07:58:33 -0600 (CST)
Subject: [gmx-users] Help to membranes pressure

> Hi everyone, Im trying to apply a pressure of -200 bar
> on a mixed of H2O and dppc, to form a bilayer
> membrane. So I modified the md.mdp, and I tried to
> follow the manual instruction, but results were very
> bad.     
> I used:
> 
> pcoupltype       = surface_tension
> compressibility  = 4.5e-5   0.005
> ref_p            = 1809.117  200.0 
> //Must I use the signs?
> 
> Because...I suposed....
> surface_tension: is coupled to the x/y dimensions of
> the box.
> First value of ref_p is surface_tension*number of
> surfaces, and I used 
> surface_tension= 9nm (-200bar - (1.013+1.013)bar/2)=
>                =9(-201.013) =  -1809.117 
>                (from 3.36 eq in the manual, 
>                 and 1 atm = 1.013bar)
> Second value of ref-p is the refence z-pressure [bar]
>                = 2000
> Two compressibility [bar-1] values are respectives to
> x/y and z directions.
>     compressibility x/y = 4.5-e5 for  water at 1 atm
> and 300 K.
>     compresibility z= 1/200bar  =  0.005 bar-1
> 
>   I will apprecite very much something of ligth,
>   Greetings...
> 
> _________________________________________________________
> Do You Yahoo!?
> La mejor conexiСn a internet y 25MB extra a tu correo por $100 al 
> mes. http://net.yahoo.com.mx _______________________________________________
> 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.
------- End of Original Message -------