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.
--Jianguo ________________________________ From: Justin Lemkul <jalem...@vt.edu> To: Jianguo Li <ljg...@yahoo.com.sg>; Discussion list for GROMACS users <gmx-users@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 -- ======================================== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ======================================== -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
