<html>
<head>
<style><!--
.hmmessage P
{
margin:0px;
padding:0px
}
body.hmmessage
{
font-size: 10pt;
font-family:Tahoma
}
--></style>
</head>
<body class='hmmessage'>
I have had a similar experience, I have not investigated it thoroughly at the moment, but I get different (identical with specific jumps possibly due to pbc) plots if I take starting structure as my input pdb file or if my starting structure is first structure of trajectory. <br><br>I think the plots would be fine if you just use g_rms -s topol.tpr -f traj.xtc <br><br><br><br>> Date: Sat, 20 Nov 2010 19:05:35 +1100<br>> From: Mark.Abraham@anu.edu.au<br>> To: gmx-users@gromacs.org<br>> Subject: Re: [gmx-users] disparity in RMSD calculation<br>> <br>> On 20/11/2010 4:54 PM, Sunita Patel wrote:<br>> > Dear Users,<br>> ><br>> > I calculated RMSD for a trajectory with same reference structure using GROMACS<br>> > and VMD. I observed completely difference plots for the same data. Please see<br>> > the attached file.<br>> ><br>> > What could be the cause for this disparity?<br>> ><br>> <br>> We can't be definitive without more detail of your two methods. The <br>> jumps look like differing PBC treatments. See trjconv -h for ways to <br>> choose how they are treated. Note that the "non-jumped" parts of the <br>> GROMACS curve agree with the VMD one.<br>> <br>> Mark<br>> -- <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/Support/Mailing_Lists/Search before posting!<br>> Please don't post (un)subscribe requests to the list. Use the <br>> www interface or send it to gmx-users-request@gromacs.org.<br>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists<br> </body>
</html>