hi all<br>i am a new user of gromacs. tried to run normal mode analysis. but failed. i did up to mdrun.but in output i am not getting .mtx file.(hesian matrix)<br>what may be the problem..can anybody help regarding this?<br>
<br><div class="gmail_quote">On Fri, Nov 21, 2008 at 8:01 PM, Maria Musgaard <span dir="ltr"><<a href="mailto:musgaard@chem.au.dk">musgaard@chem.au.dk</a>></span> wrote:<br><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
If you want to generate a kind of trajectory from the eigenvectors, I think you can use g_nmtraj and then visualise the vibration with e.g. VMD.<br>
<br>
/Maria<div><div></div><div class="Wj3C7c"><br>
<br>
<br>
Quoting Marudachalam S <<a href="mailto:msundaram@ncbs.res.in" target="_blank">msundaram@ncbs.res.in</a>>:<br>
<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
I don't know what exactly you are looking for, but normal modes can be<br>
visualized by freewares like Chemcraft, Molekel, etc. Hope it helps.<br>
<br>
Marudachalam.<br>
<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<br>
________________________________________<br>
<br>
Hi All,<br>
I am doing normal mode analysis. After getting the eigen<br>
frequencies, is there a way we can visualize the vibrational<br>
modes in gromacs. And even how to know which frequency<br>
corresponds to which mode of vibration. I saw that IED is used to<br>
visualize normal modes by integrating it with VMD. But I<br>
installed VMD on my windows machine. So I dont think there is a<br>
way to install IED on windows. Please let me if there are any<br>
softwares which can visualize normal modes if so, how to get<br>
them?<br>
<br>
Thank you<br>
abhigna<br>
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