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

bharat gupta bharat.85.monu at gmail.com
Thu Jan 27 14:10:23 CET 2011


I don't think that there is any problem in the structure .. since I am
simulating the crystal structure taken from PDB ... and I have checked the
structure generated after pdb2gmx and solvation..

Since I am reapeating the simulation again I want to know and I am on energy
minimzation step I want to know .. how can I retrieve the structure after
minimization ..

On Thu, Jan 27, 2011 at 4:16 AM, Mark Abraham <Mark.Abraham at anu.edu.au>wrote:

>  On 27/01/2011 11:11 PM, bharat gupta wrote:
>
> I used the same .mdp files that are given in the lysozyme tutorial .. Since
> I was knowing what all parameters to change .. but after energy minimization
> and equilibration steps , the graphs that I got were fine ... even the rmsd
> graph of the final structure is also fine .. I have attached the final rmsd
> graph of the structure ..
>
>
> That suggests the problem was in the structure you started the simulation
> from, like I've suggested a few times now :-)
>
> Mark
>
>
>
> On Thu, Jan 27, 2011 at 3:44 AM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
>
>>
>>
>> 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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>
>
>
> --
> 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
>
>
>
> --
> gmx-users mailing list    gmx-users at gromacs.org
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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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