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<DIV><FONT face=Arial size=2>Dear Users,</FONT></DIV>
<DIV> </DIV>
<DIV><FONT face=Arial size=2>I’ve created two different models of the same
<BR>transmembrane protein. These two models were <BR>created using
homology approach using two different <BR>templates (both with similar sequence
similarity <BR>to the sequence of the target protein). Next, I <BR>did two
separate 25ns simulations of those two <BR>obtained protein models in water and
lipid environment. <BR>RMSD value calculated using g_rms reaches about 3.5
A <BR>after 10 ns in two simulations and stays stable for <BR>the rest of the MD
time. </FONT></DIV>
<DIV> </DIV>
<DIV><FONT face=Arial size=2>What I want to do is to obtain a plot
of RMSD <BR>between those two models (model one vs model two) <BR>for each
corresponding frame of those two MD simulations<BR> (I just want to add
that the length of protein chain is <BR>different in both protein
models). Is there a script <BR>available from gromacs tools
which could be used for this? <BR>Could you give me some sugestions how to
treat this problem? <BR>Thank you in advance.<BR>Michal
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