tag:blogger.com,1999:blog-6701417360427959244.post5423175349349045598..comments2024-03-27T07:18:00.323+01:00Comments on Molecular Modeling Basics: Double bonds - banana and otherwiseJan Jensenhttp://www.blogger.com/profile/08595894308946022740noreply@blogger.comBlogger3125tag:blogger.com,1999:blog-6701417360427959244.post-4599144241388852852010-04-22T19:17:05.034+02:002010-04-22T19:17:05.034+02:00Jan,
I actually tried to use VMD, unfortunately i...Jan,<br /><br />I actually tried to use VMD, unfortunately it doesn't support GAMESS trajectory files nor output files from a MD simulation. Extended support for GAMESS is aparently planned for future versions of VMD, though.<br /><br />I think I'll do what you suggest and try to make a conversion from the GAMESS format to some other which is supported by VMD.<br /><br />Thank you very much for your help, and keep up the excellent work!<br /><br />Diegocecihttps://www.blogger.com/profile/00379998907730850012noreply@blogger.comtag:blogger.com,1999:blog-6701417360427959244.post-31907829126514191892010-04-22T08:41:25.862+02:002010-04-22T08:41:25.862+02:00Hi Diego,
This is not something I have direct exp...Hi Diego,<br /><br />This is not something I have direct experience with, but it is my impression that the <a href="http://www.ks.uiuc.edu/Research/vmd/" rel="nofollow">VMD program</a> is a popular trajectory analysis tool. <br /><br />I am not sure if VMD can read in a GAMESS trajectory file, but if you know perl then it shouldn't be too hard to reformat it (or look intro whether <a href="http://openbabel.org/wiki/Main_Page" rel="nofollow">Open Babel</a> can handle this).<br /><br />Hope this helps, and glad to hear you like the blog.Jan Jensenhttps://www.blogger.com/profile/08595894308946022740noreply@blogger.comtag:blogger.com,1999:blog-6701417360427959244.post-79566224181659228932010-04-21T20:37:57.500+02:002010-04-21T20:37:57.500+02:00Hi! I'm a graduate student in Argentina, and I...Hi! I'm a graduate student in Argentina, and I'm doing some quantum molecular dynamics simulations using GAMESS US (keyword runtyp=md + $MD group). <br />Do you know of any program or hack with which I could visualize the trajectory and/or (and at this point this would seem to be utopic) some actual data processing? <br />I tried macmolplt, but it turned out to be not very useful. <br />So far I managed to do some post processing writing perl scrips (for calculating dihedral angles from the cartesian coordinates of each frame, for example), but I would be very happy to know if there's any higher level tool I could use.<br /><br />Thank you very much in advance!<br />Excellent blog btw! Keep it up!<br /><br />Greetings<br /><br />Diego J. Alonso de Armiñocecihttps://www.blogger.com/profile/00379998907730850012noreply@blogger.com