[gmx-users] Simulation of the pure lipid bilayer
Justin A. Lemkul
jalemkul at vt.edu
Fri Apr 13 14:07:59 CEST 2012
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.
> 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
> 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
> 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
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> 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
ICTAS Doctoral Scholar
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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