<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">You may first use make_ndx to create the index file then use trjconv to save the sub-system.<div><br><div><div>On Jan 12, 2010, at 7:14 PM, zh.li wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><span class="Apple-style-span" style="border-collapse: separate; font-family: Helvetica; font-size: medium; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; "><div lang="ZH-CN" link="blue" vlink="purple"><div class="Section1"><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; text-align: justify; font-size: 10.5pt; font-family: 'Times New Roman'; "><font size="1" face="Arial"><span lang="EN-US" style="font-size: 9pt; font-family: Arial; ">Dear all,</span></font></div><p class="MsoNormal" style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; text-align: justify; font-size: 10.5pt; font-family: 'Times New Roman'; "><font size="1" face="Arial"><span lang="EN-US" style="font-size: 9pt; font-family: Arial; "> </span></font></p><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; text-align: justify; font-size: 10.5pt; font-family: 'Times New Roman'; "><font size="1" face="Arial"><span lang="EN-US" style="font-size: 9pt; font-family: Arial; "> I want to remove the water molecules in the original traj file (run.xtc) to save the space, so that I should use the command ¡°trjconv¡±. But I don¡¯t know which sub-command I should use to realize that? Does anyone here know how to do it?</span></font><font size="1" face="ËÎÌå"><span style="font-size: 9pt; font-family: ËÎÌå; ">¡¡</span></font><font size="1" face="Arial"><span lang="EN-US" style="font-size: 9pt; font-family: Arial; ">Thank you very much.</span></font></div><p class="MsoNormal" style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; text-align: justify; font-size: 10.5pt; font-family: 'Times New Roman'; "><font size="1" face="Arial"><span lang="EN-US" style="font-size: 9pt; font-family: Arial; "> </span></font></p><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; text-align: justify; font-size: 10.5pt; font-family: 'Times New Roman'; "><font size="1" face="Arial"><span lang="EN-US" style="font-size: 9pt; font-family: Arial; ">Zhenwei Li</span></font></div></div>--<span class="Apple-converted-space"> </span><br>gmx-users mailing list <a href="mailto:gmx-users@gromacs.org" style="color: blue; text-decoration: underline; ">gmx-users@gromacs.org</a><br><a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" style="color: blue; text-decoration: underline; ">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>Please search the archive at<span class="Apple-converted-space"> </span><a href="http://www.gromacs.org/search" style="color: blue; text-decoration: underline; ">http://www.gromacs.org/search</a><span class="Apple-converted-space"> </span>before posting!<br>Please don't post (un)subscribe requests to the list. Use the<span class="Apple-converted-space"> </span><br>www interface or send it to<span class="Apple-converted-space"> </span><a href="mailto:gmx-users-request@gromacs.org" style="color: blue; text-decoration: underline; ">gmx-users-request@gromacs.org</a>.<br>Can't post? Read<span class="Apple-converted-space"> </span><a href="http://www.gromacs.org/mailing_lists/users.php" style="color: blue; text-decoration: underline; ">http://www.gromacs.org/mailing_lists/users.php</a></div></span></blockquote></div><br></div></body></html>