<html><body><div style="color:#000; background-color:#fff; font-family:arial, helvetica, sans-serif;font-size:12pt"><div><span>Dear Justin.</span></div><div><span>Thanks for your explanation.</span></div><div><span>............................................................<br></span></div>In lyzozyme tutorial the radius of gyration has been plooted against simulation time (there 1000 ps).<br>When I plot the same graph, the horizontal axis is up to 500 (The number of frames for data calculation).<br>Although, the gyrate.xvg file has gyration data for these 500 frames, how can I tell gnuplot to plot gyration versus simulation time (1000 ps)?<br><br>Thanks<br>Regards<br>D.M<br><div><br></div> <div style="font-family: arial, helvetica, sans-serif; font-size: 12pt;"> <div style="font-family: times new roman, new york, times, serif; font-size: 12pt;"> <div dir="ltr"> <font face="Arial" size="2"> <hr size="1"> <b><span
style="font-weight:bold;">From:</span></b> Justin A. Lemkul <jalemkul@vt.edu><br> <b><span style="font-weight: bold;">To:</span></b> delara aghaie <d_aghaie@yahoo.com>; Discussion list for GROMACS users <gmx-users@gromacs.org> <br> <b><span style="font-weight: bold;">Sent:</span></b> Monday, 11 June 2012, 14:46<br> <b><span style="font-weight: bold;">Subject:</span></b> Re: [gmx-users] radius of gyration<br> </font> </div> <br><br><br>On 6/11/12 5:20 AM, delara aghaie wrote:<br>> Dear Gromacs users<br>> I have a question abut radius of gyration in proteins. I want to calculate it<br>> via MD simulation for calcium pump protein. Following the same method as<br>> described in justin lezozyme tutorial, we have dissolved the protein in water.<br>> I want to know that is it wise to study this parameter for this protein out of<br>> membrane and only in the box of water???<br><br>In my opinion, that's not appropriate.
The structure of a membrane protein can be highly sensitive to the environment, so any conclusions you reach would be suspect in the mind of a skeptical reviewer. Why not embed the protein in a membrane?<br><br>-Justin<br><br>-- ========================================<br><br>Justin A. Lemkul, Ph.D.<br>Research Scientist<br>Department of Biochemistry<br>Virginia Tech<br>Blacksburg, VA<br>jalemkul[at]vt.edu | (540) 231-9080<br><a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br><br>========================================<br><br><br> </div> </div> </div></body></html>