[gmx-users] Protein-POPC bilayer

Jianguo Li ljggmx at yahoo.com.sg
Fri Aug 17 03:45:27 CEST 2012

What I think is that anisotropic coupling may be 
faster in equilibrium. Suppose the protein is quite different in x and y dimensions, after  insertion, I think it is faster to get equilibrium 
the box length separately. I agree with you that semi-isotropic coupling in the first step can also do the job, but I expect it may take longer 
time to reach equilibrium. 


From: Justin Lemkul <jalemkul at vt.edu>
To: Jianguo Li <ljggmx at yahoo.com.sg>; Discussion list for GROMACS users <gmx-users at gromacs.org> 
Sent: Friday, 17 August 2012, 9:19
Subject: Re: [gmx-users] Protein-POPC bilayer

On 8/16/12 9:14 PM, Jianguo Li wrote:
> After inserting the protein, the equilibrium box length in the x and y dimension should be different, so you need anisotropic pressure coupling during the 1st step. After equilibrium, the ratio of box length in x,y is fixed, so you can use semi-isotropic method.

Most pre-equilibrated bilayers have (roughly) equivalent x and y box dimensions.  Why do you think they should inherently be different?

In my experience, anisotropic coupling leads to major deformations in the x-y plane, taking a bilayer that is initially a square (roughly) in the x-y plane and turning it into a rectangle.  I'd be very curious to hear Peter's answer to this question.  I used to use anisotropic coupling, but now I use semiisotropic exclusively.


-- ========================================

Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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