[gmx-users] regarding rmsd and md

[Tsjerk Wassenaar]

Hi Priya,

Inspect your trajectory visually and you'll probably see the cause of the
high RMSD. Also check the mailing list on the topic.

Whether you'll see micelle formation depends on many factors. The time
scale, for example.

Cheers,

Tsjerk

On Jan 7, 2012 7:02 AM, "priya thiyagarajan" <priya.thiyagarajan09 at gmail.com>
wrote:

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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