<DIV> </DIV><DIV> </DIV><SPAN>On 03/05/12, <B class=name>mu xiaojia </B><muxiaojia2010@gmail.com> wrote:</SPAN>
<BLOCKQUOTE style="BORDER-LEFT: #00f 1px solid; PADDING-LEFT: 13px; MARGIN-LEFT: 0px" class=iwcQuote cite=mid:CABSFTFpkNHkwGANYCs=+Jn=mXe6YShwYRZLQwim0J2PYcXrA6g@mail.gmail.com type="cite"><FONT class=Apple-style-span size=4>Dear gmx users,</FONT>
<DIV><FONT class=Apple-style-span size=4><br /></FONT></DIV><DIV><FONT class=Apple-style-span size=4>I have a question about using the trjconv -pbc options before analyzing my trajectory. It's stated by Justin's tutorial that:</FONT></DIV><DIV><FONT class=Apple-style-span size=4><br /></FONT></DIV><DIV><SPAN style="FONT-FAMILY: Arial" class=Apple-style-span>
<P><FONT class=Apple-style-span size=4>"use trjconv to account for any periodicity in the system. The protein will diffuse through the unit cell, and may appear to "jump" across to the other side of the box. To account for such actions, issue the following:</FONT></P><PRE><FONT class=Apple-style-span size=4>trjconv -s md_0_1.tpr -f md_0_1.xtc -o md_0_1_noPBC.xtc -pbc mol -ur compact"</FONT></PRE><PRE><FONT class=Apple-style-span size=4>(<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/09_analysis.html" target=1 >http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/09_analysis.html</A></FONT></PRE><PRE><FONT class=Apple-style-span size=4>)</FONT></PRE><PRE><FONT class=Apple-style-span size=4><br /></FONT></PRE><PRE><FONT class=Apple-style-span size=4>But for my system, I study the short peptides' aggregation, I have many short peptides(not one or two single proteins) and waters, when I use -pbc nojump to treat my trajectory, it only gives me correct short peptides(no across out of the box), but the water is quite diffused. (I guess it is different with the tutorial since on it the protein is 1 or 2 polymers)</FONT></PRE><PRE><FONT class=Apple-style-span size=4><br /></FONT></PRE><PRE><FONT class=Apple-style-span size=4>So (1)how should I analyze such results if I want to study both short peptides(correct coordinates, no crossings) and waters(diffused and crossed box)?</FONT></PRE></SPAN></DIV></BLOCKQUOTE>
<DIV> </DIV><DIV>That entirely depends on what you are trying to observe. You may find you need multiple representations of the trajectory for different purposes.</DIV><DIV> </DIV><BLOCKQUOTE style="BORDER-LEFT: #00f 1px solid; PADDING-LEFT: 13px; MARGIN-LEFT: 0px" class=iwcQuote cite=mid:CABSFTFpkNHkwGANYCs=+Jn=mXe6YShwYRZLQwim0J2PYcXrA6g@mail.gmail.com type="cite">
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<DIV><SPAN style="FONT-FAMILY: Arial" class=Apple-style-span><PRE><FONT class=Apple-style-span size=4>(2) I tried all the pbc options(even try them one after another, like mol first, nojump second), currently no clues of how to get both peptides and waters correct at the same time.　Command for correct protein but incorrect waters' coordinates is:</FONT></PRE><PRE><FONT class=Apple-style-span size=4><SPAN style="FONT-FAMILY: Arial; WHITE-SPACE: normal; FONT-SIZE: small" class=Apple-style-span><PRE><FONT class=Apple-style-span size=4>trjconv -s md_0_1.tpr -f md_0_1.xtc -o md_0_1_noPBC.xtc -pbc nojump</FONT></PRE>
<PRE><FONT class=Apple-style-span size=4><br /></FONT></PRE><PRE><FONT class=Apple-style-span size=4>Thanks very much, I appreciate any suggestions.</FONT></PRE></SPAN></FONT></PRE></SPAN></DIV></DIV></BLOCKQUOTE>
<DIV> </DIV><DIV>If molecules diffuse across the periodic boundaries, you cannot have a single representation that is both compact and lacks jumps.</DIV><DIV> </DIV><DIV>Mark</DIV>