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Hi,<br><br>In principle g_traj -oxt -com would give you a trajectory with the COM's, you would then need a pdb or tpr<br>with the COM's as well. But in 4.0.5 there is a bug in g_traj when writing many COM's. This will be fixed in 4.0.6.<br><br>A, maybe simpler, solution, if your system runs fast, it to add COM virtual-sites to your atomistic topology,<br>which will then also appear in your trajectory.<br>Look in the manual on how to construct such virtual sites.<br><br>Berk <br><br><hr id="stopSpelling">Date: Wed, 4 Nov 2009 21:11:49 +0530<br>From: jmondal2004@yahoo.co.in<br>Subject: Re: [gmx-users] g_angle between center of mass of three groups<br>To: gmx-users@gromacs.org<br><br><table border="0" cellpadding="0" cellspacing="0"><tbody><tr><td style="font-family: inherit; font-style: inherit; font-variant: inherit; font-weight: inherit; font-size: inherit; line-height: inherit; font-size-adjust: inherit; font-stretch: inherit; -x-system-font: none;" valign="top">Thanks, But I guess the g_angle -ov option will give me an average angle for many different groups. <br>That will not be same as the angle between center of masses of different group .<br>For example If I have a molecule CH3-CH2-CH3, g_angle -ov can give me an average over angle H-C-H and C-C-C . But what I want is the angle CH3-CH2-CH3 .<br><br>So, I was wondering whether you can clarify a bit on how I can get it.<br>Thanks<br>Jagannath<br><br><br><br>--- On <b>Wed, 4/11/09, Mark Abraham <i><Mark.Abraham@anu.edu.au></i></b> wrote:<br><blockquote style="margin-left: 5px; padding-left: 5px;"><br>From: Mark Abraham <Mark.Abraham@anu.edu.au><br>Subject: Re: [gmx-users] g_angle between center of mass of three groups<br>To: "Discussion list for GROMACS users" <gmx-users@gromacs.org><br>Date:
Wednesday, 4 November, 2009, 9:00 AM<br><br><div class="ecxplainMail">jagannath mondal wrote:<br>> Hi,<br>> <br>> I know that g_dist gives the distance between the center of masses of two groups. But, I wanted to know whether it is possible to calculate angle between center of masses of three groups or not . I am not sure whether g_angle can calculate the angle between center of masses of three groups. If not, In that case, can anyone suggest suggest any other alternative ?<br><br>You should start by reading g_angle -h and g_sgangle -h. g_angle will calculate the average over a group of angles, which is similar to what you want.<br><br>Mark<br>_______________________________________________<br>gmx-users mailing list <a href="http:///mc/compose?to=gmx-users@gromacs.org">gmx-users@gromacs.org</a><br><a href="http://lists.gromacs.org/mailman/listinfo/gmx-users">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>Please search the archive at <a href="http://www.gromacs.org/search">http://www.gromacs.org/search</a> before posting!<br>Please don't post (un)subscribe requests to the list. Use the www interface or send it to <a href="http:///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/mailing_lists/users.php">http://www.gromacs.org/mailing_lists/users.php</a><br></div></blockquote></td></tr></tbody></table><br>
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