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

[Justin A. Lemkul]

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>
>>

-- 
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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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