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<DIV><FONT size=2 face=Arial><SPAN class=218405310-13052011>Dear
gmx-users,</SPAN></FONT></DIV>
<DIV><FONT size=2 face=Arial><SPAN class=218405310-13052011>I'm simulating a
homodimeric protein obtained by homology modelling. In the .pdb file, I have 2
chain identifiers (A and B). I used Gromacs 4.0.7 to prepare the .gro files for
simulation (up to nvt); then I was forced to switch to Gromacs 4.5.4 on another
machine to continue with npt and full MD. I used the files from Gromacs 4.0.7 to
continue, and it seems to me that all went OK. Now I have the files from the
full MD, and I started to analyze them.</SPAN></FONT></DIV>
<DIV><FONT size=2 face=Arial><SPAN class=218405310-13052011>I used g_rmsf to
analyze the fluctuations of the residues, and I found that the results for the
two subunits of the protein are superimposed. In the file .gro that comes from
the MD as well as in the file .gro that comes from the npt MD made with Gromacs
4.5.4, the number of residues of the second subunit does not continue after the
first subunit (i.e. after the last 359th residue of the first subunit, I see
that the first residue of the second subunit is numbered 1 instead of 360), but
in the nvt file produced by Gromacs 4.0.7 that I provided to Gromacs
4.5.4, the numbering of the two subunits is
sequential. </SPAN></FONT></DIV>
<DIV><FONT size=2 face=Arial><SPAN class=218405310-13052011>My questions
are:</SPAN></FONT></DIV>
<DIV><FONT size=2 face=Arial><SPAN class=218405310-13052011>1) why Gromacs 4.5.4
changed the numbering of the residues in the two subunits, even if it started
from a .gro file?</SPAN></FONT></DIV>
<DIV><FONT size=2 face=Arial><SPAN class=218405310-13052011>2) Does this affect
the result of the MD?</SPAN></FONT></DIV>
<DIV><FONT size=2 face=Arial><SPAN class=218405310-13052011>3) how can I
separate, or renumber, the resulting .gro files in order to have a graph in
which the fluctuations are not superimposed?</SPAN></FONT></DIV>
<DIV><FONT size=2 face=Arial><SPAN class=218405310-13052011>Thank you very much
and regards</SPAN></FONT></DIV>
<DIV><FONT size=2 face=Arial><SPAN
class=218405310-13052011>Anna</SPAN></FONT></DIV>
<DIV> </DIV>
<DIV align=left>
<DIV dir=ltr align=left><FONT size=2
face=Arial>__________________________________________________________________</FONT></DIV>
<DIV align=left><FONT size=2 face=Arial>Anna Marabotti, Ph.D.</FONT></DIV>
<DIV align=left><FONT size=2 face=Arial>Laboratory of Bioinformatics and
Computational Biology</FONT></DIV>
<DIV align=left><FONT size=2 face=Arial>Institute of Food Science -
CNR</FONT></DIV>
<DIV align=left><FONT size=2 face=Arial>Via Roma, 64</FONT></DIV>
<DIV align=left><FONT size=2 face=Arial>83100 Avellino</FONT></DIV>
<DIV align=left><FONT size=2 face=Arial>Phone: +39 0825 299651</FONT></DIV>
<DIV align=left><FONT size=2 face=Arial>Fax: +39 0825 781585</FONT></DIV>
<DIV align=left><FONT size=2 face=Arial>E-mail: <A
title=mailto:amarabotti@isa.cnr.it
href="mailto:amarabotti@isa.cnr.it">amarabotti@isa.cnr.it</A></FONT></DIV>
<DIV align=left><FONT size=2 face=Arial>Skype account: annam1972</FONT></DIV>
<DIV align=left><FONT size=2 face=Arial>Web site: <A
title=http://bioinformatica.isa.cnr.it/anna/anna.htm
href="http://bioinformatica.isa.cnr.it/anna/anna.htm">http://bioinformatica.isa.cnr.it/anna/anna.htm</A></FONT></DIV>
<DIV align=left><FONT size=2 face=Arial></FONT> </DIV>
<DIV align=left><FONT size=2 face=Arial>"When a man with a gun meets a man with
a pen, the man with the gun is a dead man"</FONT></DIV>
<DIV align=left><FONT size=2 face=Arial>(Roberto Benigni, about Roberto
Saviano)</FONT></DIV></DIV>
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