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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.<?xml:namespace prefix = o ns =
"urn:schemas-microsoft-com:office:office" /><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></BODY></HTML>