[gmx-users] regarding rmsd and md

priya thiyagarajan priya.thiyagarajan09 at gmail.com
Sat Jan 7 07:01:40 CET 2012

hello sir,

I performed dynamics for my lipopeptide...

After md i thought of calculating rmsd...
i did my md for 4ns..
when i plot graph for rmsd, i got plot til 2.2ns

i dono why it came like this..
can anyone tell me why it is like this..

and also i like to clarify one doubt...

If i do dynamics for 20surfactin, at the end of simulation how my result ll
be..i.e.  whether any  miscelle formation at the end or ll my surfactin ll
be like how it is at the begining..

Thanking you,
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