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

Justin A. Lemkul jalemkul at vt.edu
Thu Jan 27 12:44:26 CET 2011



bharat gupta wrote:
> I generated the secondary structure profile of structure retrieved from 
> the last frame of the simulation ... In that profile those amino acids 
> that are shown as loops in VMD doesnot have any secondary structure 
> assignment ... it means that during simulation the structure got changed 
> some how ... and It's really surprising ?? ... Can u tell me where can 
> the fault be as I am planning to do the simulation again and this time I 
> will check the structure after every step .. but for that I want to know 
> how can I save the structure after every step say for eg. after energy 
> minimization ..
> 

Secondary structure is dependent upon the chosen force field and the .mdp 
settings.  Since you've posted neither, there's no way to tell what might be to 
blame.

You can save more frequently by setting the proper output controls.  Read in the 
manual about the nst* options and set the accordingly.

-Justin

> On Thu, Jan 27, 2011 at 8:35 PM, Justin A. Lemkul <jalemkul at vt.edu 
> <mailto:jalemkul at vt.edu>> wrote:
> 
> 
> 
>     Mark Abraham wrote:
> 
> 
> 
>         On 01/27/11, *bharat gupta * <bharat.85.monu at gmail.com
>         <mailto:bharat.85.monu at gmail.com>> wrote:
> 
>             I actually don't understand exactly what u are asking ..
>             since I am not an expert with gromacs..
> 
> 
>         Please leave the old context for the discussion in future
>         emails. Only you are paying so much attention to your work that
>         you can be sure of remembering things :-)
> 
>         If your simulation started with these strands unfolded, then
>         your problem is somewhere else. However, you have to be able to
>         tell us what was the initial conformation, and when your "first
>         trajectory frame" (per last email) happened in the simulation.
> 
> 
>     I would also add that VMD does a fairly poor job sometimes of
>     guessing secondary structure.  So if no beta strand was present in
>     the very first frame, that doesn't necessarily mean the secondary
>     structure wasn't stable, it just means VMD didn't display it properly.
> 
>     -Justin
> 
>         Mark
> 
> 
>             I don't know when is was written .. Here are some lines from
>             the log files of simulation ...
>             Statistics over 1500001 steps using 300001 frames
> 
>               Energies (kJ/mol)
>                      Angle    Proper Dih. Ryckaert-Bell.          LJ-14
>                 Coulomb-14
>                7.35090e+03    4.37413e+02    3.60104e+03    5.26705e+03
>                2.58894e+04
>                    LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip.
>                  Potential
>                1.05399e+05   -2.92853e+03   -6.79288e+05   -1.07015e+05
>               -6.41286e+05
>                Kinetic En.   Total Energy    Temperature Pres. DC (bar)
>             Pressure (bar)
>                1.03484e+05   -5.37802e+05    3.00003e+02   -2.37485e+02
>                1.02890e+00
>               Constr. rmsd
>                0.00000e+00
> 
>                      Box-X          Box-Y          Box-Z
>                7.42618e+00    7.42618e+00    7.42618e+00
> 
>               Total Virial (kJ/mol)
>                3.44183e+04    3.40020e+01   -1.17357e+01
>                3.42160e+01    3.45369e+04   -2.46337e+01
>               -1.16644e+01   -2.48479e+01    3.44949e+04
> 
>               Pressure (bar)
>                1.99809e+00    9.48448e-02    4.57909e-01
>                7.74354e-02    4.97824e-01    1.84797e+00
>                4.52125e-01    1.86535e+00    5.90776e-01
> 
>               Total Dipole (D)
>               -1.86272e+02    4.46310e+01    2.08554e+02
> 
>                  T-Protein  T-non-Protein
>                2.99904e+02    3.00013e+02
> 
> 
>             M E G A - F L O P S   A C C O U N T I N G
> 
> 
>             There were in total 1502 frames (as shown in VMD )...
>             I don't know about how it compared with the coordinates of
>             the structure that I gave to grompp
> 
>             --------
> 
>             Pls guide
> 
> 
> 
> 
>             -- 
>             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>
>             <mailto:monu46010 at yahoo.com <mailto:monu46010 at 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 <http://vt.edu> | (540) 231-9080
>     http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> 
>     ========================================
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> 
> 
> -- 
> 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
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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