[gmx-users] Simulation of the pure lipid bilayer

[rajat desikan]

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?

On Fri, Apr 13, 2012 at 5:28 PM, Justin A. Lemkul <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 | (540) 231-9080
> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>
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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
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