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

[bharat gupta]

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 ..

On Thu, Jan 27, 2011 at 8:35 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:

>
>
> Mark Abraham wrote:
>
>>
>>
>> On 01/27/11, *bharat gupta * <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>
>>>
>>>
> --
> ========================================
>
> 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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-- 
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
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