[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
>>
>> ========================================
>> --
>> 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
>
>
>
> --
> 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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