Re: [gmx-users] Re: change in structure after simulation

[Justin A. Lemkul]

bharat gupta wrote:

Hi,

I did a simulation of 5ns ... after viewing the trajectory in VMD , some 
loop regions seems to be stretched like a straight wire.. But when I 
made a movie using trjconv and viewed in pymol.. the structure seems to 
be fine.. So, shall I continue my analysis assuming the structure to be 
fine ...




http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions

-Justin


--
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 : monu46...@yahoo.com 



--


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
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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[gmx-users] Re: change in structure after simulation

[bharat gupta]

Hi,

I did a simulation of 5ns ... after viewing the trajectory in VMD , some
loop regions seems to be stretched like a straight wire.. But when I made a
movie using trjconv and viewed in pymol.. the structure seems to be fine..
So, shall I continue my analysis assuming the structure to be fine ...

-- 
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 : monu46...@yahoo.com
-- 
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