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Hello, Elijah:
Thank you for correcting my mistake. I use the input as you suggested. It
works perfect. I got the RSMD values from the four runs.
Thank you very much.
Have a good day!
Bo
On Sun, 31 Oct 2004 00:29:23 -0600 Elijah Gregory wrote:
> You need to load in each trajectory with four trajin commands in
> one input file and then issue an rms command. This should calculate
> the rmsd from the first structure of the first run for all four
> trajectories in succession.
>
> What you are doing is taking the first run and calculating the rmsd
> from the first structure in that run, then loading in the second run
> and calculating the rmsd from the first structure of *that* run, etc.
> Obviously the "distance" between the first structure in a run and the
> first structure in a run will be zero.
>
> Try using this input file:
>
> model1-3mdCA-rms.in
>
> trajin model1-3-md1.crd
> trajin model1-3-md2.crd
> trajin model1-3-md2a.crd
> trajin model1-3-md2b.crd
> rms first out model1-3md-backbone.rms .CA time 0.2
> strip :WAT
> go
>
> Hope this helps,
>
> Elijah Gregory
>
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Received on Sun Oct 31 2004 - 18:53:00 PST
