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<DIV><FONT size=2 face=Arial><SPAN class=421251715-04072011>Dear
users,</SPAN></FONT></DIV>
<DIV><FONT size=2 face=Arial><SPAN class=421251715-04072011>following Tsjerk'
suggestions, I simulate the protein which had some problems in periodic distance
violations in a triclinic box, using instead a rhombic dodecahedron box
created with the options:</SPAN></FONT></DIV>
<DIV><FONT size=2 face=Arial><SPAN
class=421251715-04072011></SPAN></FONT> </DIV>
<DIV><FONT size=2 face=Arial><SPAN class=421251715-04072011>editconf -f prot.gro
-o prot_boxdod.gro -bt dodecahedron -d 1.5 -c</SPAN></FONT></DIV>
<DIV><FONT size=2 face=Arial><SPAN
class=421251715-04072011></SPAN></FONT> </DIV>
<DIV><FONT size=2 face=Arial><SPAN class=421251715-04072011>Minimization, PR-NVT
and PR-NPT went OK (no error messages, potential energy after minimization of
about -1e+6). I run 30 ns full MD (no PR).</SPAN></FONT></DIV>
<DIV><FONT size=2 face=Arial><SPAN class=421251715-04072011>At the end of the
production MD, I would like to repeat the g_mindist analysis, so I can be sure
my system does not suffer again of a periodic distance
violation.</SPAN></FONT></DIV>
<DIV><FONT size=2 face=Arial><SPAN class=421251715-04072011>I performed
g_mindist on 4 different systems, and these are my results:</SPAN></FONT></DIV>
<DIV><FONT size=2 face=Arial><SPAN class=421251715-04072011>1) on the resulting
trajectory: on average, the distance between two periodic distances calculated
on the entire protein (option = 1) is > 3 nm. However, until 10 ns I can see
several "spikes" going down to < 0.1 nm</SPAN></FONT></DIV>
<DIV><FONT size=2 face=Arial><SPAN class=421251715-04072011>2) on the resulting
trajectory, applying trjconv -pbc nojump before g_mindist: on average, the
distance is < 0.1 nm</SPAN></FONT></DIV>
<DIV><FONT size=2 face=Arial><SPAN class=421251715-04072011>3) on the resulting
trajectory, applying trjconv -pbc whole -ur compact before g_mindist: the same
as 1) (perfectly superimposable)</SPAN></FONT></DIV>
<DIV><FONT size=2 face=Arial><SPAN class=421251715-04072011>4) on the resulting
trajectory, applying trjconv -pbc whole -ur compact, then trjconv -pbc nojump,
before g_mindist calculation: the same as 2) (perfectly
superimposable)</SPAN></FONT></DIV>
<DIV><FONT size=2 face=Arial><SPAN class=421251715-04072011>My questions
are:</SPAN></FONT></DIV>
<DIV><FONT size=2 face=Arial><SPAN class=421251715-04072011>1) do I have to
transform in some (other) way the trajectory before calculating g_mindist? Do I
have to calculate g_mindist in another way (eg. using a different group for
calculations)?</SPAN></FONT></DIV>
<DIV><FONT size=2 face=Arial><SPAN class=421251715-04072011>2) given these
results, can I consider this trajectory suitable for analysis? (maybe excluding
the first 10 ns)</SPAN></FONT></DIV>
<DIV><FONT size=2 face=Arial><SPAN class=421251715-04072011>3) If not, what can
I do more to have a suitable trajectory?</SPAN></FONT></DIV>
<DIV><FONT size=2 face=Arial><SPAN
class=421251715-04072011></SPAN></FONT> </DIV>
<DIV><FONT size=2 face=Arial><SPAN class=421251715-04072011>Many thanks for any
suggestions, I'm quite frustrating for not understanding where the problem comes
from...</SPAN></FONT></DIV>
<DIV><FONT size=2 face=Arial><SPAN
class=421251715-04072011>Anna</SPAN></FONT></DIV>
<DIV><FONT size=2 face=Arial></FONT> </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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