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<DIV><FONT size=2 face=Arial><SPAN class=859575509-20092011>Dear
gmx-users,</SPAN></FONT></DIV>
<DIV><FONT size=2 face=Arial><SPAN class=859575509-20092011>I'm doing several
simulations of a monomeric protein with different ligands. I had
several frustrating experiences because I found that at the end of simulations,
I found that my complexes violate the minimum periodic image
distance.</SPAN></FONT></DIV>
<DIV><FONT size=2 face=Arial><SPAN
class=859575509-20092011></SPAN></FONT> </DIV>
<DIV><FONT size=2 face=Arial><SPAN class=859575509-20092011>I'm using Gromacs
4.5.3 and for all my simulations I set a triclinic box with the
command:</SPAN></FONT></DIV>
<DIV><FONT size=2 face=Arial><SPAN class=859575509-20092011>editconf -f prot.gro
-o prot_box.gro -bt triclinic -d 1.5 -c</SPAN></FONT></DIV>
<DIV><FONT size=2 face=Arial><SPAN class=859575509-20092011>I think that this
dimension is sufficient since I'm using rcoul= 1.0 and rvdw=1.4 nm. I'm
currently using amber99sb force field with tip3p water; the system was
neutralized with Na.</SPAN></FONT></DIV>
<DIV><FONT size=2 face=Arial><SPAN class=859575509-20092011>I have minimized (to
Emtol=500) my system, equilibrated with 20 psec NVT+100 ps NPT (I checked the
energies, and they were all constant), then submitted to a full MD for 30
ns.</SPAN></FONT></DIV>
<DIV><FONT size=2 face=Arial><SPAN
class=859575509-20092011></SPAN></FONT> </DIV>
<DIV><FONT size=2 face=Arial><SPAN class=859575509-20092011>When I had a look at
the trajectory using VMD, I saw that the protein goes partially out of the box,
therefore I used:</SPAN></FONT></DIV>
<DIV><FONT size=2 face=Arial><SPAN class=859575509-20092011>trjconv -f
prot_full.xtc -s prot_full.tpr -o prot_fullC.xtc -pbc nojump (selection:
System=0)</SPAN></FONT></DIV>
<DIV><FONT size=2 face=Arial><SPAN class=859575509-20092011>and I analysed the
new trajectory with:</SPAN></FONT></DIV>
<DIV><FONT size=2 face=Arial><SPAN class=859575509-20092011>g_mindist -f
prot_fullC.xtc -s prot_full.tpr -od prot_fullC_mindist.xvg -pi (selection:
Protein=1)</SPAN></FONT></DIV>
<DIV><FONT size=2 face=Arial><SPAN
class=859575509-20092011></SPAN></FONT> </DIV>
<DIV><FONT size=2 face=Arial><SPAN class=859575509-20092011>The graph shows that
the minimum periodic image is < 1.4 nm for a large part of the trajectories
(and even < 1.0 nm in some cases), therefore I'm assuming that the protein
interacts with its periodic images (and that the trajectories must be thrown
away...)</SPAN></FONT></DIV>
<DIV><FONT size=2 face=Arial><SPAN
class=859575509-20092011></SPAN></FONT> </DIV>
<DIV><FONT size=2 face=Arial><SPAN class=859575509-20092011></SPAN></FONT><FONT
size=2 face=Arial><SPAN class=859575509-20092011>I would like to ask some
questions. Maybe they are trivial, but I hope the answers will be useful not for
me only.</SPAN></FONT></DIV>
<DIV><FONT size=2 face=Arial><SPAN class=859575509-20092011>1) Am I doing
correctly the analyses? Am I indicating correctly the System (option 0) to
perform the nojump option, and the Protein (option 1) to analyse the minimum
distance?</SPAN></FONT></DIV>
<DIV><FONT size=2 face=Arial><SPAN class=859575509-20092011>2) What could be the
causes for these recurrent periodic image violations in my system(s)? Why does a
protein "go out" of the box? Can I argue that the box is too small? Can I argue
that the system is not fully relaxed before the production MD? What are
the analyses that I can make to assess these conditions before doing the
MD? </SPAN></FONT></DIV>
<DIV><FONT size=2 face=Arial><SPAN class=859575509-20092011></SPAN></FONT><FONT
size=2 face=Arial><SPAN class=859575509-20092011>3) What are the
solutions? Do I have to increase the box dimensions? Do I have to change
the box type? In another case, I solved the problem using a rhombic dodecahedron
box, so is this a problem recurrent only for triclinic box, or not? Can a longer
stabilization of the system avoid this problem? </SPAN></FONT></DIV>
<DIV><FONT size=2 face=Arial><SPAN
class=859575509-20092011></SPAN></FONT> </DIV>
<DIV><FONT size=2 face=Arial><SPAN class=859575509-20092011>In summary, I'd like
to know if there is a way to predict the risk of having a similar problem
looking at the system BEFORE simulation is made (and time is wasted...), and if
it depends on some incorrect setting of the system (maybe some .mpd option?), or
not.</SPAN></FONT></DIV>
<DIV><FONT size=2 face=Arial><SPAN
class=859575509-20092011></SPAN></FONT> </DIV>
<DIV><FONT size=2 face=Arial><SPAN class=859575509-20092011>Thank you very much
for your answers.</SPAN></FONT></DIV>
<DIV><FONT size=2 face=Arial><SPAN
class=859575509-20092011>Anna</SPAN></FONT></DIV>
<DIV><FONT size=2 face=Arial><SPAN
class=859575509-20092011></SPAN></FONT> </DIV>
<DIV 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 (Italy)</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>Email: <A
href="mailto:anna.marabotti@isa.cnr.it">anna.marabotti@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 page: <A
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 a gun is a dead man"</FONT></DIV>
<DIV align=left><FONT size=2 face=Arial>(Roberto Benigni, about Roberto
Saviano)</FONT></DIV>
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