----- Original Message -----<br>From: Birgit Hischenhuber <birgit.hischenhuber@meduniwien.ac.at><br>Date: Wednesday, June 2, 2010 0:44<br>Subject: [gmx-users] Visualizing of a peptide in a water box - using trjconv<br>To: gmx-users@gromacs.org<br><br><span xmlns:o="urn:schemas-microsoft-com:office:office" xmlns:w="urn:schemas-microsoft-com:office:word" xmlns:st1="urn:schemas-microsoft-com:office:smarttags" xmlns="http://www.w3.org/TR/REC-html40"><p> <meta http-equiv="Content-Type" content="text/html; charset=us-ascii"> <meta name="Generator" content="Microsoft Word 11 (filtered medium)"> <o:smarttagtype namespaceuri="urn:schemas-microsoft-com:office:smarttags" name="City"> <o:smarttagtype namespaceuri="urn:schemas-microsoft-com:office:smarttags" name="place"> <!--[if !mso]>
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<![endif]--> <style> <!-- /* Style Definitions */ p.MsoNormal, li.MsoNormal, div.MsoNormal {margin:0cm; margin-bottom:.0001pt; font-size:12.0pt; font-family:"Times New Roman";} a:link, span.MsoHyperlink {color:blue; text-decoration:underline;} a:visited, span.MsoHyperlinkFollowed {color:purple; text-decoration:underline;} span.E-MailFormatvorlage17 {mso-style-type:personal-compose; font-family:Arial; color:windowtext;} @page Section1 {size:595.3pt 841.9pt; margin:70.85pt 70.85pt 2.0cm 70.85pt;} div.Section1 {page:Section1;} --> </style> <table><tbody><tr><td link="blue" vlink="purple" lang="DE"><p> </p><div class="Section1"> <p class="MsoNormal"><font face="Arial" size="2"><span style="font-size: 10pt; font-family: Arial;"><font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font>Hi,<o:p></o:p></span></font></p> <p class="MsoNormal"><font face="Arial" size="2"><span style="font-size: 10pt; font-family: Arial;"><o:p><font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font> </o:p></span></font></p> <p class="MsoNormal"><font face="Arial" size="2"><span style="font-size: 10pt; font-family: Arial;" lang="EN-GB"><font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font>I simulate a peptide in a water box with some ions to get a neutral solution. I want to visualize the peptide in the water box.<o:p></o:p></span></font></p> <p class="MsoNormal"><font face="Arial" size="2"><span style="font-size: 10pt; font-family: Arial;" lang="EN-GB"><font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font>I want that the peptide is in the center of the box, but also have a look at the water.<o:p></o:p></span></font></p> <p class="MsoNormal"><font face="Arial" size="2"><span style="font-size: 10pt; font-family: Arial;" lang="EN-GB"><o:p><font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font> </o:p></span></font></p> <p class="MsoNormal"><font face="Arial" size="2"><span style="font-size: 10pt; font-family: Arial;" lang="EN-GB"><font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font>Therefore I tried two things:<o:p></o:p></span></font></p> <p class="MsoNormal"><font face="Arial" size="2"><span style="font-size: 10pt; font-family: Arial;" lang="EN-GB"><o:p><font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font> </o:p></span></font></p> <p class="MsoNormal"><font face="Arial" size="2"><span style="font-size: 10pt; font-family: Arial;" lang="EN-GB"><font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font>trjconv –f a.trr –o b.xtc –s c.tpr –skip 10 –pbc mol –<st1:city w:st="on"><st1:place w:st="on">ur</st1:place></st1:city> compact –center –fit progressive<o:p></o:p></span></font></p> <p class="MsoNormal"><font face="Arial" size="2"><span style="font-size: 10pt; font-family: Arial;" lang="EN-GB"><o:p><font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font> </o:p></span></font></p> <p class="MsoNormal"><font face="Arial" size="2"><span style="font-size: 10pt; font-family: Arial;" lang="EN-GB"><font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font>Visualizing it with VMD I see the peptide centering in the middle of the box, but the water get during the time holes.<o:p></o:p></span></font></p> <p class="MsoNormal"><font face="Arial" size="2"><span style="font-size: 10pt; font-family: Arial;" lang="EN-GB"><o:p><font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font> </o:p></span></font></p> <p class="MsoNormal"><font face="Arial" size="2"><span style="font-size: 10pt; font-family: Arial;" lang="EN-GB"><font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font>So I checked the mailing list and find some inputs and tried it with two steps:<o:p></o:p></span></font></p> <p class="MsoNormal"><font face="Arial" size="2"><span style="font-size: 10pt; font-family: Arial;" lang="EN-GB"><o:p><font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font> </o:p></span></font></p> <p class="MsoNormal"><font face="Arial" size="2"><span style="font-size: 10pt; font-family: Arial;" lang="EN-GB"><font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font>trjconv –f a.trr –o b.xtc –s c.tpr –pbc mol –<st1:city w:st="on"><st1:place w:st="on">ur</st1:place></st1:city> compact<o:p></o:p></span></font></p> <p class="MsoNormal"><font face="Arial" size="2"><span style="font-size: 10pt; font-family: Arial;" lang="EN-GB"><font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font>trjconv –f b.xtc –o d.xtc –s c.tpr –skip 10 –center –fit progressive<o:p></o:p></span></font></p> <p class="MsoNormal"><br><font face="Arial" size="2"><span style="font-size: 10pt; font-family: Arial;" lang="EN-GB"><o:p></o:p></span></font></p><p class="MsoNormal"><font face="Arial" size="2"><span style="font-size: 10pt; font-family: Arial;" lang="EN-GB"><o:p>I don't think -ur or -fit are useful for your problem. I suspect something like <br></o:p></span></font></p><p class="MsoNormal"><br><font face="Arial" size="2"><span style="font-size: 10pt; font-family: Arial;" lang="EN-GB"><o:p></o:p></span></font></p><p class="MsoNormal"><span xmlns:o="urn:schemas-microsoft-com:office:office" xmlns:w="urn:schemas-microsoft-com:office:word" xmlns:st1="urn:schemas-microsoft-com:office:smarttags" xmlns="http://www.w3.org/TR/REC-html40"><font face="Arial" size="2"><span style="font-size: 10pt; font-family: Arial;" lang="EN-GB">trjconv -center<br></span></font></span></p><p class="MsoNormal"><span xmlns:o="urn:schemas-microsoft-com:office:office" xmlns:w="urn:schemas-microsoft-com:office:word" xmlns:st1="urn:schemas-microsoft-com:office:smarttags" xmlns="http://www.w3.org/TR/REC-html40"><font face="Arial" size="2"><span style="font-size: 10pt; font-family: Arial;" lang="EN-GB"></span></font></span><font face="Arial" size="2"><span style="font-size: 10pt; font-family: Arial;" lang="EN-GB"><o:p>trjconv -pbc mol</o:p></span></font></p><p class="MsoNormal"><br><font face="Arial" size="2"><span style="font-size: 10pt; font-family: Arial;" lang="EN-GB"><o:p></o:p></span></font></p><p class="MsoNormal"><font face="Arial" size="2"><span style="font-size: 10pt; font-family: Arial;" lang="EN-GB"><o:p>is what you want, perhaps even in one pass. Obviously, check trjconv -h for info - it suggests the combination of the above...</o:p></span></font></p><p class="MsoNormal"><br><font face="Arial" size="2"><span style="font-size: 10pt; font-family: Arial;" lang="EN-GB"><o:p></o:p></span></font></p><p class="MsoNormal"><font face="Arial" size="2"><span style="font-size: 10pt; font-family: Arial;" lang="EN-GB"><o:p>Mark<br></o:p></span></font></p><p class="MsoNormal"><font face="Arial" size="2"><span style="font-size: 10pt; font-family: Arial;" lang="EN-GB"><o:p><br></o:p></span></font></p> <p class="MsoNormal"><font face="Arial" size="2"><span style="font-size: 10pt; font-family: Arial;" lang="EN-GB"><font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font>at this try I get a peptide in the center of the box and during the time the pepide moves to the edge of the box and I consider that the box rotate around the peptide.<o:p></o:p></span></font></p> <p class="MsoNormal"><font face="Arial" size="2"><span style="font-size: 10pt; font-family: Arial;" lang="EN-GB"><o:p><font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font> </o:p></span></font></p> <p class="MsoNormal"><font face="Arial" size="2"><span style="font-size: 10pt; font-family: Arial;" lang="EN-GB"><font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font>Is there a possibility that my peptide stays in the center of the box and the water doesn’t get any holes?<o:p></o:p></span></font></p> <p class="MsoNormal"><font face="Arial" size="2"><span style="font-size: 10pt; font-family: Arial;" lang="EN-GB"><o:p><font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font> </o:p></span></font></p> <p class="MsoNormal"><font face="Arial" size="2"><span style="font-size: 10pt; font-family: Arial;" lang="EN-GB"><font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font>Thanks a lot for your helps!<o:p></o:p></span></font></p> <p class="MsoNormal"><font face="Arial" size="2"><span style="font-size: 10pt; font-family: Arial;" lang="EN-GB"><o:p><font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font> </o:p></span></font></p> <p class="MsoNormal"><font face="Arial" size="2"><span style="font-size: 10pt; font-family: Arial;" lang="EN-GB"><font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font>---</span></font><span lang="EN-GB"><o:p></o:p></span></p> <p class="MsoNormal"><font face="Times New Roman" size="3"><span style="font-size: 12pt;" lang="EN-GB"><font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font> <o:p></o:p></span></font></p> <p class="MsoNormal"><font face="Times New Roman" size="2"><span style="font-size: 10pt;" lang="EN-GB"><font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font>DI Birgit Hischenhuber</span></font><span lang="EN-GB"><o:p></o:p></span></p> <p class="MsoNormal"><font face="Times New Roman" size="2"><span style="font-size: 10pt;" lang="EN-GB"><font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font>Unit for Medical Statistics and Informatics </span></font><span lang="EN-GB"><o:p></o:p></span></p> <p class="MsoNormal"><font face="Times New Roman" size="2"><span style="font-size: 10pt;" lang="EN-GB"><font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font>Section for Biomedical Computersimulation and Bioinformatics</span></font><span lang="EN-GB"><o:p></o:p></span></p> <p class="MsoNormal"><font face="Times New Roman" size="3"><span style="font-size: 12pt;"><o:p><font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font> </o:p></span></font></p> </div> </td></tr></tbody></table> </o:smarttagtype></o:smarttagtype></p></span> > -- <br>> gmx-users mailing list gmx-users@gromacs.org<br>> http://lists.gromacs.org/mailman/listinfo/gmx-users<br>> Please search the archive at http://www.gromacs.org/search <br>> before posting!<br>> Please don't post (un)subscribe requests to the list. 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