<table cellspacing="0" cellpadding="0" border="0" ><tr><td valign="top" style="font: inherit;">Dear Mark<br>I will try to be more specific.<br><br>In the case I have 4 chains in a simulation box, by typing g_gyrate -f traj.xtc -s topol.tpr -nmol 4 I take the following:<br><br> Group 0 ( System) has 180elements<br> Group 1 ( AAA) has 45 elements<br> Group 2 ( BAA) has 45 elements<br> Group 3 ( CAA) has 45 elements<br> Group 4 ( DAA) has 45 elements<br>Select group:<br><br>By choosing here the Group 0, GROMACS
calculates the Rg for each chain and then calculates the average Rg.<br><br>Now I have the same system but with a substrate. I want to calculate again the average Rg for these 4 chains without taking into acount the substrate. So, how can I select in the following only the 4 chains and find again the average Rg? <br><br>Group 0 ( System) has 680elements<br>Group 1 ( ZZZ) has 500elements<br>Group 2 ( AAA) has 45 elements<br>Group 3 ( BAA) has 45 elements<br>Group 4 ( CAA) has 45 elements<br>Group 5
( DAA) has 45 elements<br>Select group:<br><br>Notice that I don't want to find the Rg over the union of the chains, but the local Rg of each chain and then to take the average. <br><br>I hope know you understand<br><br>Many thanks<br>Chrysostomos<br><br><br><br><br>--- Στις <b>Τρίτ., 12/10/10, ο/η Mark Abraham <i><mark.abraham@anu.edu.au></i></b> έγραψε:<br><blockquote style="border-left: 2px solid rgb(16, 16, 255); margin-left: 5px; padding-left: 5px;"><br>Από: Mark Abraham <mark.abraham@anu.edu.au><br>Θέμα: Re: [gmx-users] g_gyrate<br>Προς: "Discussion list for GROMACS users" <gmx-users@gromacs.org><br>Ημερομηνία: Τρίτη, 12 Οκτώβριος 2010, 13:47<br><br><div id="yiv876468993">I'm not sure what the problem is. If you want to merge groups to get the radius of gyration over the union of those groups, then you need to use
make_ndx on your previous .ndx file to generate such a group.<br><br>Mark<br><br>----- Original Message -----<br>From: "C. Batistakis" <cbatiss@yahoo.gr><br>Date: Tuesday, October 12, 2010 21:44<br>Subject: [gmx-users] g_gyrate<br>To: gromacs <gmx-users@gromacs.org><br><br><table border="0" cellpadding="0" cellspacing="0"><tbody><tr><td style="font: inherit;" valign="top"><font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font>Dear all<br><font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font><br><font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font>I have the following system. Substrate with 3696 particles and 4 polymer chains with 45 beads/chain. After typing g_gyrate, I have the following option:<br><font style="font-style: normal;
font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font><br><font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font>Group 0 ( System) has 680 elements<br><font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font>Group 1 ( ZZZ) has 500 elements<br><font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font>Group 2 ( AAA) has 45 elements<br><font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font>Group 3
( BAA) has 45 elements<br><font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font>Group 4 ( CAA) has 45 elements<br><font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font>Group 5 ( DAA) has 45 elements<br><font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font>Select a group:<br><font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font><br><font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">>
</font>Can someone tell me how can I calculate the average radius of gyration only from the groups 2,3,4,5 of the previous system? <br><font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font><br><font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font>Thanks in advance<br><font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font>Chrysostomos<br><font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font><br></td></tr></tbody></table><font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font><br>> -- <br>> gmx-users mailing list gmx-users@gromacs.org<br>>
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