[gmx-users] Protein-POPC bilayer

[Dallas Warren]

Not directly related to bilayers, but our work with liquid phases has found some interesting things with anisotropic versus isotropic.  Basically, even though anisotropic allows things to structure without constraints to how they want to be, there is some artifacts that drive it too far, beyond what is reasonable and you get severe box distortion and failure.  Will be saying a little on that in an upcoming paper ....

Catch ya,

Dr. Dallas Warren
Drug Discovery Biology
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3052
dallas.warren at monash.edu
+61 3 9903 9304
---------------------------------
When the only tool you own is a hammer, every problem begins to resemble a nail. 

> -----Original Message-----
> From: gmx-users-bounces at gromacs.org [mailto:gmx-users-
> bounces at gromacs.org] On Behalf Of Justin Lemkul
> Sent: Friday, 17 August 2012 12:33 PM
> To: Discussion list for GROMACS users
> Subject: Re: [gmx-users] Protein-POPC bilayer
> 
> 
> 
> On 8/16/12 10:21 PM, Mark Abraham wrote:
> > On 17/08/2012 11:46 AM, Justin Lemkul wrote:
> >>
> >>
> >> On 8/16/12 9:43 PM, Jianguo Li wrote:
> >>> 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.
> >>>
> >>
> >> What I generally see is basically the opposite.  Using anisotropic
> pressure
> >> coupling leads to a steady change in box dimensions, but this is not
> the case
> >> with semiisotropic coupling.  It depends, I suppose, on how one
> produces the
> >> membrane protein system - adequate deletion of lipids can
> accommodate for a
> >> protein of any shape without affecting box vectors.
> >
> > Or depends on the force field or lipid?
> >
> 
> Certainly a possibility.  I think that the statement in the manual
> makes it
> pretty clear though that the algorithm itself is likely responsible for
> at least
> some of the observed deformations - "Beware that anisotropic scaling
> can lead to
> extreme deformation of the simulation box."
> 
> -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 at 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-request at gromacs.org.
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists