Hi.
You will need a visualization program like VMD to get a 3D representation of your system. After reading in the .gro file, you can edit representation details and take pictures. Greetings, Felix Von: [email protected] [mailto:[email protected]] Im Auftrag von cuong nguyen Gesendet: Dienstag, 10. Januar 2012 07:39 An: [email protected]; Discussion list for GROMACS users Betreff: Re: [gmx-users]-Snapshots Thanks a lot Justin. I have just used trjconv -dump with the command "trjconv -s NVT_final2ns.tpr -f NVT_final2ns -o trjconv.gro -dump 1" to extract a frame. However, I still do not know how to get the snapshot like a 3D picture <data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAAFkAAABUCAYAAADplZtxAAAKE mlDQ1BJQ0MgUHJvZmlsZQAAeAHVlmdYVMcax+ec7Y22y9Jh6b13kN6b9CoqywJLXZelY0MkG IGIIiJNETBUBaNSJBZEFAtBQAELGpAgoMRgAVRU7gGeJ8m9z823++W+87wzvzPlPTPvzIc/A KQPTC43HhYAIIGTzPNxsmUEBYcwcOMAAlhABHRAZrKSuDZeXu7gH21pFJmN2APNtVj/OO2/D whGRCaxAIC8kOHwiCRWAsIXEdZhcXnJCP+G8GBaMhdheK2fxkM2iPDtNWZv8Pgah2/wwvocP x87AFBoAPBkJpPHBoCEnBAwUllsJA5JB2EdTkQMB+EwhC1Z0cwIhE8hrJGQsGON+xFWCf9bH PbfmMkM/zMmk8n+kzfOgqxEfmwfk8SNZ2asf/wvq4T4FCRf67aWdXIkx98XaWmISwJ74ADck cIAXkAPKbpAJzkyHTkzAHY7uBm8GHZ0MsMGuaVIDYYLh6WlwdDT0dVbG/6/sbX3ubHZ94/W3 x1Ex//Vx6UDYGqP3H3tX33h4gB0IDkTI/zVp1APAH8QAO1ZrBRe6kY85LkAgEFePT+STTEgD eSBCtBEsmgEzIE1kllX4An8QDDYBlggGiQAHkgDu8A+kAvywWFwDJSDKlALGsBZcB50gMvgO rgF7oFBMAKeggkwDV6DBbAEViAIwkEUiAqJQTKQIqQO6UEmkCXkALlDPlAwFAaxIQ6UAu2C9 kP5UBFUDlVDjdBP0CXoOnQHGoIeQ5PQHPQO+gyjYDJMg6VgJVgbNoFtYDfYD94Ks+FEOBPOg Q/BpXANfAZuh6/D9+AReAJ+DS+iAIqEoqNkUZooE5QdyhMVgopC8VB7UHmoElQNqgXVhepDP UBNoOZRn9BYNBXNQGuizdHOaH80C52I3oMuQJejG9Dt6F70A/QkegH9DUPBSGLUMWYYF0wQh o1Jw+RiSjB1mDbMT> . Please help me! Many thanks Cuong Nguyen 2012/1/10 Justin A. Lemkul <[email protected]> cuong nguyen wrote: Dear Users, Please let me know if we can get snapshot from GROMACS. I am using version 4.4. The final configuration of any simulation is written to a coordinate file by default. You can extract any frame from your trajectory using trjconv -dump. -Justin -- ======================================== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 <tel:%28540%29%20231-9080> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ======================================== -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists -- Nguyen Van Cuong PhD student - Curtin University of Technology Mobile: (+61) 452213981
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