[gmx-users] Simulation of the pure lipid bilayer

[Justin A. Lemkul]

rajat desikan wrote:
> Justin,I have a question. If we download files from Peter Tieleman's 
> website, all you get are .gro files, and no cpt files. Then what should 
> one do? Continue using the velocities in the .gro file?
> 

Run a new equilibration.  IIRC, those structures are the product of very short 
(2 ns or so) simulations produced many years ago.  More equilibration is 
expected for more modern simulations.

-Justin

> On Fri, Apr 13, 2012 at 5:28 PM, Justin A. Lemkul <jalemkul at vt.edu 
> <mailto:jalemkul at vt.edu>> wrote:
> 
> 
> 
>     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
> 
>     -- 
>     ==============================__==========
> 
>     Justin A. Lemkul
>     Ph.D. Candidate
>     ICTAS Doctoral Scholar
>     MILES-IGERT Trainee
>     Department of Biochemistry
>     Virginia Tech
>     Blacksburg, VA
>     jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
>     http://www.bevanlab.biochem.__vt.edu/Pages/Personal/justin
>     <http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
> 
>     ==============================__==========
>     -- 
>     gmx-users mailing list    gmx-users at gromacs.org
>     <mailto:gmx-users at gromacs.org>
>     http://lists.gromacs.org/__mailman/listinfo/gmx-users
>     <http://lists.gromacs.org/mailman/listinfo/gmx-users>
>     Please search the archive at
>     http://www.gromacs.org/__Support/Mailing_Lists/Search
>     <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
>     <mailto:gmx-users-request at gromacs.org>.
>     Can't post? Read http://www.gromacs.org/__Support/Mailing_Lists
>     <http://www.gromacs.org/Support/Mailing_Lists>
> 
> 
> 
> 
> -- 
> Rajat Desikan (Ph.D Scholar)
> Prof. K. Ganapathy Ayappa's Lab (no 13),
> Dept. of Chemical Engineering,
> Indian Institute of Science, Bangalore

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

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

========================================