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On 20/10/2010 9:07 PM, leila karami wrote:
<blockquote
cite="mid:AANLkTik8+QmMxiY6N2KmvWv4xNPP7T9HT638u8cRVWuP@mail.gmail.com"
type="cite">
<p style="font-family: arial,helvetica,sans-serif;"
class="MsoNormal"><font size="2"><span style="line-height:
115%;">Hi gromacs
users</span></font></p>
<p style="font-family: arial,helvetica,sans-serif;"
class="MsoNormal"><font size="2"><span style="line-height:
115%;"><br>
</span></font></p>
<p style="font-family: arial,helvetica,sans-serif;"
class="MsoNormal"><font size="2"><span style="line-height:
115%;">I study
simulation of protein-dna interaction using gromacs. After
full md simulation,
because of diffusion of one strand of dna to edge of box, I
used trjconv -f old.xtc
–o new.xtc –s *.tpr -pbc nojump -ur compact –center. By this
way my first
problem is solved.</span></font></p>
<p class="MsoListParagraphCxSpFirst" style="text-indent: -0.25in;
font-family: arial,helvetica,sans-serif;"><font size="2"><span
style="line-height: 115%;"><span>1)<span style="font-style:
normal; font-variant: normal; font-weight: normal;
line-height: normal; font-size-adjust: none;
font-stretch: normal;"> </span></span></span><span
dir="LTR"></span><span style="line-height: 115%;"><span> </span>Should
I use new xtc file for analysis section?</span></font></p>
</blockquote>
That depends what you want to observe, and whether periodicity is
relevant to that observation.<br>
<blockquote
cite="mid:AANLkTik8+QmMxiY6N2KmvWv4xNPP7T9HT638u8cRVWuP@mail.gmail.com"
type="cite">
<p class="MsoListParagraphCxSpLast" style="text-indent: -0.25in;
font-family: arial,helvetica,sans-serif;"><font size="2"><span
style="line-height: 115%;"><span>2)<span style="font-style:
normal; font-variant: normal; font-weight: normal;
line-height: normal; font-size-adjust: none;
font-stretch: normal;"> </span></span></span><span
dir="LTR"></span><span style="line-height: 115%;">When I see
new
xtc file, there isn’t any water molecule in interface
between protein and dna(where
as there were water molecules interface between protein and
dna, before full md
simulation). I want to survey water mediated hydrogen bond
between protein and
dna. Do –pbc nojump cause to this problem?</span></font></p>
</blockquote>
Probably. Probably what you want is to center on the combined
protein+DNA group (need to make an index group) and then put the COM
of all residues in the box. That will mean your water region and
surrounds of interest are contiguous.<br>
<br>
Mark<br>
<br>
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