[gmx-users]-Snapshots

[Rausch, Felix]

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: gmx-users-bounces at gromacs.org
[mailto:gmx-users-bounces at gromacs.org] Im Auftrag von cuong nguyen
Gesendet: Dienstag, 10. Januar 2012 07:39
An: jalemkul at vt.edu; 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
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whGRCaxAIC8kOHwiCRWAsIXEdZhcXnJCP+G8GBaMhdheK2fxkM2iPDtNWZv8Pgah2/wwvocP
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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 <jalemkul at vt.edu>



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

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Nguyen Van Cuong

PhD student - Curtin University of Technology

Mobile: (+61) 452213981

 

 

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