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

priya thiyagarajan priya.thiyagarajan09 at gmail.com
Thu Jan 12 07:39:07 CET 2012

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..

it ll be helpful for me..

Thanking you,
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