[gmx-users] regarding rmsd plot obtained for less time

[Mark Abraham]

On 12/01/2012 5:39 PM, priya thiyagarajan wrote:
> hello sir,
>
> I did dynamics for 5ns for my protein. i submitted my run in cluster.. 
> i got my output.. when i go for rmsd and gyrate analysis i got plot 
> for only 1.2ns out of 5ns..
>
> i dono what is the problem..
>
> is this because of low runtime in cluster..
> even i gave 200hours in cluster..
>
> i searched in gromacs list.. but i didnt get answer for my query..
>
> can anyone please help me with your answer..

Nobody can help you given the available information. Please consider the 
advice here: http://www.gromacs.org/Support

Mark