Hi Nicolas,
I'll try that too since I am somewhat familiar with VMD scripting to I may equilibrate a 2X 2Y 1Z membrane like you specified, and have a script find a timeframe where lipid composition fits what I need. Thanks, -Shay -----Original Message----- From: [email protected] [mailto:[email protected]] On Behalf Of Nicolas Sapay Sent: Wednesday, June 03, 2009 15:23 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] Resizing heterogeneous membrane (POPG/POPE mixture) Shay Amram a écrit : > > Dear GROMACS users, > > I have been trying to expand a membrane by a non-integer multiplier > (for example X1.5). This can be done using > > *genbox -cs Membrane.gro -o Expanded_membrane.gro box 1.5X 1.5Y Z*** > > This has worked very good with _homogenous_ membranes, and only very > short equilibrium times were required to re-equilibrate the membrane > (~10-20ns). > > Now I am trying to deal the same way with _heterogeneous_ membrane > (POPG/POPE mixture, Mikko Karttunen et. al). > > When trying to invoke the above command to the POPG/POPE membrane I > get a membrane with different compositions of lipids in the upper and > lower leaflets. > > This happens (so I suspect) because the arrangement of lipids in each > leaflet is somewhat different so that the molecules that "get' to be > multiplied do not conserve the > > same ratio of different lipids as in the original structure (which has > ratio of 1:3 POPG/POPE). > > Is there a way to multiply the membrane by a _non-integer_ number AND > somehow conserve the ratio of different lipid species too? > > Or at the very least, to have both upper and lower leaflets identical > after multiplication? (This, too, would help immensely). > This is quite a difficult task unfortunately. Personally, I create a membrane patch larger than the one I want (e.g. 2x 2y 1z), load the gro file into VMD, then cut a patch the size/composition I need. That means doing selections like: set sel [atomselect top "same resid as (x<... and x>... and y<... and y>...)"] Checking the number of lipids in each layer: [atomselect top "resname DOPG and name P1 and z>... and (same resid as (x<... and x>... and y<... and y>...))"] num [atomselect top "resname DOPG and name P1 and z<... and (same resid as (x<... and x>... and y<... and y>...))"] num Completing the selection by manually adding the residues I need: set sel [atomselect top "same resid as (x<... and x>... and y<... and y>...) or resid ..."] Saving the coordinates: animate write pdb sel $sel This is a tidy task and some equilibration is still required after that. Basic knowledge of TCL/VMD scripting languages may be required to facilitate/automate the work. Nicolas > > Thanks, > > -Shay > > ------------------------------------------------------------------------ > > _______________________________________________ > gmx-users mailing list [email protected] > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [email protected]. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php
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