<table cellspacing="0" cellpadding="0" border="0" ><tr><td valign="top" style="font: inherit;">Thanks for the reply.<br>In fact I had the trajectory with water but then I removed it to have smaller size of files. the point is that It didn't complain or crash when I was using that trajectory, choosing water in the groups selecting. but it didn't also generate any output. that is why I asked that ...<br><br>Anyway since I have gro files time to time, I think I will cat all the gro file and use that for analysis of h_bond. <br>Fahimeh<br><br>--- On <b>Fri, 9/17/10, David van der Spoel <i><spoel@xray.bmc.uu.se></i></b> wrote:<br><blockquote style="border-left: 2px solid rgb(16, 16, 255); margin-left: 5px; padding-left: 5px;"><br>From: David van der Spoel <spoel@xray.bmc.uu.se><br>Subject: Re: [gmx-users] g_hbond<br>To: "Discussion list for GROMACS users" <gmx-users@gromacs.org><br>Date: Friday, September 17, 2010, 9:37 PM<br><br><div
class="plainMail">On 9/17/10 5:37 PM, Justin A. Lemkul wrote:<br>><br>><br>> Fahimeh Baftizadeh Baghal wrote:<br>>> hello,<br>>> I have a trajectory generated by gromacs in which I excluded water and<br>>> there is only protein, now I like to see how does the number of h_bond<br>>> between water and protein change during the trajectory. In fact when I<br>>> use g_hbond I can choose the water and protein but I was wondering<br>>> where does the information about water come from??<br>><br>> Certainly you can choose whatever groups are present (either from<br>> default groups or from those in an index file), but I would imagine the<br>> command will either fail or simply identify that there are no hydrogen<br>> bond donors or acceptors within what would otherwise be water.<br>><br>> If you have not saved the coordinates for water, you cannot run any<br>> command to analyze properties
related to or involving water.<br><br>In theory you could get an approximate number from analyzing what polar <br>groups are not hydrogen bonded intramolecularly. There is not ready tool <br>to do this. The quickest solution is probably to rerun the simulation. <br>In most cases human time is more valuable than computer time.<br><br>><br>> -Justin<br>><br>>> thank you in advance for your time<br>>><br>>> Fahimeh<br>><br><br><br>-- <br>David.<br>________________________________________________________________________<br>David van der Spoel, PhD, Professor of Biology<br>Dept. of Cell and Molecular Biology, Uppsala University.<br>Husargatan 3, Box 596, 75124 Uppsala, Sweden<br>phone: 46 18 471 4205 fax: 46 18 511 755<br><a ymailto="mailto:spoel@xray.bmc.uu.se" href="/mc/compose?to=spoel@xray.bmc.uu.se">spoel@xray.bmc.uu.se</a> <a
ymailto="mailto:spoel@gromacs.org" href="/mc/compose?to=spoel@gromacs.org">spoel@gromacs.org</a> <a href="http://folding.bmc.uu.se" target="_blank">http://folding.bmc.uu.se</a><br>++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++<br>-- <br>gmx-users mailing list <a ymailto="mailto:gmx-users@gromacs.org" href="/mc/compose?to=gmx-users@gromacs.org">gmx-users@gromacs.org</a><br><a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>Please search the archive at <a href="http://www.gromacs.org/Support/Mailing_Lists/Search" target="_blank">http://www.gromacs.org/Support/Mailing_Lists/Search</a> before posting!<br>Please don't post (un)subscribe requests to the list. Use the <br>www interface or send it to <a ymailto="mailto:gmx-users-request@gromacs.org"
href="/mc/compose?to=gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.<br>Can't post? Read <a href="http://www.gromacs.org/Support/Mailing_Lists" target="_blank">http://www.gromacs.org/Support/Mailing_Lists</a><br></div></blockquote></td></tr></table><br>