hi all 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) what may be the problem..can anybody help regarding this?
On Fri, Nov 21, 2008 at 8:01 PM, Maria Musgaard <[EMAIL PROTECTED]> wrote: > 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. > > /Maria > > > > Quoting Marudachalam S <[EMAIL PROTECTED]>: > > I don't know what exactly you are looking for, but normal modes can be >> visualized by freewares like Chemcraft, Molekel, etc. Hope it helps. >> >> Marudachalam. >> >> >>> ________________________________________ >>> >>> Hi All, >>> I am doing normal mode analysis. After getting the eigen >>> frequencies, is there a way we can visualize the vibrational >>> modes in gromacs. And even how to know which frequency >>> corresponds to which mode of vibration. I saw that IED is used to >>> visualize normal modes by integrating it with VMD. But I >>> installed VMD on my windows machine. So I dont think there is a >>> way to install IED on windows. Please let me if there are any >>> softwares which can visualize normal modes if so, how to get >>> them? >>> >>> Thank you >>> abhigna >>> _______________________________________________ >>> gmx-users mailing list gmx-users@gromacs.org >>> http://www.gromacs.org/mailman/listinfo/gmx-users >>> Please search the archive at http://www.gromacs.org/search before >>> posting! >>> Please don't post (un)subscribe requests to the list. Use the >>> www interface or send it to [EMAIL PROTECTED] >>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >>> >>> >> _______________________________________________ >> gmx-users mailing list gmx-users@gromacs.org >> http://www.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at http://www.gromacs.org/search before >> posting! >> Please don't post (un)subscribe requests to the list. Use the >> www interface or send it to [EMAIL PROTECTED] >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >> >> > > > ---------------------------------------------------------------- > This message was sent using IMP, the Internet Messaging Program. > > _______________________________________________ > gmx-users mailing list gmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use thewww interface > or send it to [EMAIL PROTECTED] > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php >
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