[gmx-users] Regarding g_analyze

Justin A. Lemkul jalemkul at vt.edu
Fri Jan 21 04:52:24 CET 2011

bharat gupta wrote:
> It means that  rmsd plot is stable .. I am trying to run the trajectory 
> in windows using VMD and for that i followed what was said in past 
> thread of gmx discussion list but I am not able to run the trajectory 
> and for that I have posted another question regarding that jus 5 mins back..
> Also if u can shed some light of this very important issue ... that to 
> learn simulation in gromacs and to analyze the things needed for our 
> analysis .. what exactly do we need to do .. as in my case i am 
> following ur tutorial and asking doubts in the gmx user list but I am 
> not able to get many things still ... like analysing the plots and 
> graphs and how to tell whch value is correct at what particular time for 
> how much simulation time ?? ... pls do ket me know how can I have a firm 
> grip in this regard...

You need to develop a set of measurable quantities that your simulation should 
address long before you even begin building the system.  Then, once you identify 
what you will measure and how you will measure it, design the simulation system 
and run the MD.  What you define as "correct" depends entirely upon what is 
being measured, what the system is, and what the question is that you're asking.

No one on this list is going to be able (or willing, usually) to help you work 
through your project, so do invest some time with textbook and literature 
reading to get a sense of what you should be doing.


> -- 
> Bharat
> Ph.D. Candidate
> Room No. : 7202A, 2nd Floor
> Biomolecular Engineering Laboratory
> Division of Chemical Engineering and Polymer Science
> Pusan National University
> Busan -609735
> South Korea
> Lab phone no. - +82-51-510-3680, +82-51-583-8343
> Mobile no. - 010-5818-3680
> E-mail : monu46010 at yahoo.com <mailto:monu46010 at yahoo.com>


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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