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<DIV dir=ltr align=left><SPAN class=816203602-19032009><FONT face=Arial
color=#0000ff size=2>No, the molecule has not gone out the side of the box and
not entered the other side. If you check the solvent on the opposite side
of the box, you will notice that there is a big hole that exactly matches up
with the DNA fragment that is sticking out. Use the pbc options in VMD to
display neighbouring images of the box, that will make it much more explicit
what is going on.</FONT></SPAN></DIV>
<DIV dir=ltr align=left><SPAN class=816203602-19032009><FONT face=Arial
color=#0000ff size=2></FONT></SPAN> </DIV>
<DIV dir=ltr align=left><SPAN class=816203602-19032009><FONT face=Arial
color=#0000ff size=2>Unless otherwise noted, the analsysis programs and
intelligent enough to realise where things are located.</FONT></SPAN></DIV>
<DIV dir=ltr align=left><SPAN class=816203602-19032009><FONT face=Arial
color=#0000ff size=2></FONT></SPAN> </DIV>
<DIV dir=ltr align=left><SPAN class=816203602-19032009><FONT face=Arial
color=#0000ff size=2>Remember, with a periodic box, all things are
relative. The location of the boundaries of the base unit are totally
arbitary, you can move them around at your will to visualise, it makes no
difference to how things are calculated or handled by the
software.</FONT></SPAN></DIV><!-- Converted from text/plain format -->
<P><FONT size=2>Catch ya,<BR><BR>Dr. Dallas Warren<BR>Department of
Pharmaceutical Biology and Pharmacology<BR>Pharmacy and Pharmaceutical Sciences,
Monash University<BR>381 Royal Parade, Parkville VIC
3010<BR>dallas.warren@pharm.monash.edu.au<BR>+61 3 9903
9167<BR>---------------------------------<BR>When the only tool you own is a
hammer, every problem begins to resemble a nail.</FONT> </P>
<DIV> </DIV><BR>
<BLOCKQUOTE dir=ltr
style="PADDING-LEFT: 5px; MARGIN-LEFT: 5px; BORDER-LEFT: #0000ff 2px solid; MARGIN-RIGHT: 0px">
<DIV class=OutlookMessageHeader lang=en-us dir=ltr align=left>
<HR tabIndex=-1>
<FONT face=Tahoma size=2><B>From:</B> gmx-users-bounces@gromacs.org
[mailto:gmx-users-bounces@gromacs.org] <B>On Behalf Of </B>Pablo
Umazano<BR><B>Sent:</B> Thursday, 19 March 2009 10:19 AM<BR><B>To:</B>
gmx-users@gromacs.org<BR><B>Subject:</B> [gmx-users] g_rdf
program<BR></FONT><BR></DIV>
<DIV></DIV>
<DIV><FONT face=Arial size=2>
<P class=MsoNormal
style="MARGIN: 0cm 0cm 0pt; LINE-HEIGHT: 150%; TEXT-ALIGN: justify"><SPAN
lang=EN-US
style="FONT-SIZE: 10pt; LINE-HEIGHT: 150%; FONT-FAMILY: Arial; mso-ansi-language: EN-US">Hello,
I am relatively new to gromacs and I really would appreciate help with the
following question.<o:p></o:p></SPAN></P>
<P class=MsoNormal
style="MARGIN: 0cm 0cm 0pt; LINE-HEIGHT: 150%; TEXT-ALIGN: justify"><SPAN
lang=EN-US
style="FONT-SIZE: 10pt; LINE-HEIGHT: 150%; FONT-FAMILY: Arial; mso-ansi-language: EN-US"><o:p> </o:p></SPAN></P>
<P class=MsoNormal
style="MARGIN: 0cm 0cm 0pt; LINE-HEIGHT: 150%; TEXT-ALIGN: justify"><SPAN
lang=EN-US
style="FONT-SIZE: 10pt; LINE-HEIGHT: 150%; FONT-FAMILY: Arial; mso-ansi-language: EN-US">I
have used a coarse-grained model to represent a DNA fragment with
approximately 50 nm of length. I have run a Langevin dynamics simulation of
DNA with ions NA+ and CL- to study their distribution of around DNA. During
simulation I used the option to remove the center of mass motion (default
option) because when there are no external forces the <I
style="mso-bidi-font-style: normal">com</I> linear moment must be
conserved.<o:p></o:p></SPAN></P>
<P class=MsoNormal
style="MARGIN: 0cm 0cm 0pt; LINE-HEIGHT: 150%; TEXT-ALIGN: justify"><SPAN
lang=EN-US
style="FONT-SIZE: 10pt; LINE-HEIGHT: 150%; FONT-FAMILY: Arial; mso-ansi-language: EN-US">Now,
I want study the redistribution of ions around DNA when an external electric
field is applied. My doubt is the following: when external electric field is
applied, should I remove the center of mass motion? I thought that the answer
was no, then I tried the following option:<o:p></o:p></SPAN></P>
<P class=MsoNormal
style="MARGIN: 0cm 0cm 0pt; LINE-HEIGHT: 150%; TEXT-ALIGN: justify"><SPAN
lang=EN-US
style="FONT-SIZE: 10pt; LINE-HEIGHT: 150%; FONT-FAMILY: Arial; mso-ansi-language: EN-US"><o:p> </o:p></SPAN></P>
<P class=MsoNormal
style="MARGIN: 0cm 0cm 0pt; LINE-HEIGHT: 150%; TEXT-ALIGN: justify"><SPAN
lang=EN-US
style="FONT-SIZE: 10pt; LINE-HEIGHT: 150%; FONT-FAMILY: Arial; mso-ansi-language: EN-US">comm_mode<SPAN
style="mso-spacerun: yes"> </SPAN>none<o:p></o:p></SPAN></P>
<P class=MsoNormal
style="MARGIN: 0cm 0cm 0pt; LINE-HEIGHT: 150%; TEXT-ALIGN: justify"><SPAN
lang=EN-US
style="FONT-SIZE: 10pt; LINE-HEIGHT: 150%; FONT-FAMILY: Arial; mso-ansi-language: EN-US"><o:p> </o:p></SPAN></P>
<P class=MsoNormal
style="MARGIN: 0cm 0cm 0pt; LINE-HEIGHT: 150%; TEXT-ALIGN: justify"><SPAN
lang=EN-US
style="FONT-SIZE: 10pt; LINE-HEIGHT: 150%; FONT-FAMILY: Arial; mso-ansi-language: EN-US">but
half of DNA goes out of the box during simulation (I see this with ngmx and in
out.gro) and nothing enters the another side.<o:p></o:p></SPAN></P>
<P class=MsoNormal
style="MARGIN: 0cm 0cm 0pt; LINE-HEIGHT: 150%; TEXT-ALIGN: justify"><SPAN
lang=EN-US
style="FONT-SIZE: 10pt; LINE-HEIGHT: 150%; FONT-FAMILY: Arial; mso-ansi-language: EN-US">I
know gromacs use pbc to calculate the interactions between particles, but I
wonder if g_rdf program considers that part of DNA is out the box to calculate
the radial function distribution of ions around DNA.<o:p></o:p></SPAN></P>
<P class=MsoNormal
style="MARGIN: 0cm 0cm 0pt; LINE-HEIGHT: 150%; TEXT-ALIGN: justify"><SPAN
lang=EN-US
style="FONT-SIZE: 10pt; LINE-HEIGHT: 150%; FONT-FAMILY: Arial; mso-ansi-language: EN-US"><o:p> </o:p></SPAN></P>
<P class=MsoNormal
style="MARGIN: 0cm 0cm 0pt; LINE-HEIGHT: 150%; TEXT-ALIGN: justify"><SPAN
lang=EN-US
style="FONT-SIZE: 10pt; LINE-HEIGHT: 150%; FONT-FAMILY: Arial; mso-ansi-language: EN-US">Thank.<o:p></o:p></SPAN></P>
<P class=MsoNormal
style="MARGIN: 0cm 0cm 0pt; LINE-HEIGHT: 150%; TEXT-ALIGN: justify"><SPAN
lang=EN-US
style="FONT-SIZE: 10pt; LINE-HEIGHT: 150%; FONT-FAMILY: Arial; mso-ansi-language: EN-US">Pablo<o:p></o:p></SPAN></P></FONT></DIV></BLOCKQUOTE></BODY></HTML>