[gmx-users] how to extend 1ns Unfolding simulation to 6ns

[Justin A. Lemkul]

ravi sharma wrote:
> Hello guys,
> 
> i have a problem that on unfolding simulation my protein unfolds quickly 
> within 500ps 70% and rest stable in entire simulation as this is the 
> state of equilibrium in which gromacs equilibrate the system ,so we 
> wann'a do an equilibrium MD for 1ns than have to extend to 6ns, it looks 
> like hard because when we start a extended simulation,it takes previous 
> .tpr file,
> is anyone have idea how to perform this kind of simulation ?????
> 
> 

Have a look here:

http://wiki.gromacs.org/index.php/Doing_Restarts

There are two options - tpbconv and grompp.  Using tpbconv requires the previous 
.tpr file, but using grompp does not.  The only reason that would be "hard" is 
if you had deleted the previous .tpr file (which can probably be regenerated, 
anyway).

-Justin

> 
> regards,
> 
> 
> Ravi Datta Sharma
> Lecturer,
> Bioinformatics,
> Department of Microbiology,
> CCS Unversity,
> Meerut
>                                                          
> 
> 
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-- 
========================================

Justin A. Lemkul
Graduate Research Assistant
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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