[gmx-users] Simulation of the pure lipid bilayer

[Justin A. Lemkul]

James Starlight wrote:
> Dear Gromacs Users!
> 
> 
> I want to perform simulation of the pure bilayer surrounded by water. 
> I'm using already pre-equilibrated bilayers as the initial structure. 
> During conversion pdb-> gro -> pdb the velocities from initial 
> equilibration runs of the structure were lost. Should I start generating 

Relying on a .gro file to maintain velocities is a bad idea.  The values 
contained therein lack sufficient precision to be reliable.  You should be using 
.cpt files to continue runs to preserve the previous ensemble, thus making the 
choice of coordinate file format irrelevant.

> this velocities in my production run ( gen_Vel= yes) or i must do 
> equilibration instead first to generate velocities? Finally what length 

A production run should not start with newly generated velocities.  Doing so 
destroys the initial equilibration, and if you haven't taken care to preserve 
that anyway, you should probably just start over and make proper use of .cpt files.

> should this equilibration be to provide reasonable velocities for 
> futrher MD run if I would avoild long equilibration period because of 
> suitability of my initial model?
> 

There is no universal answer to this question.  It depends on your criteria for 
convergence and contents of the system, among other considerations.

-Justin

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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