[gmx-users] Re: change in the secondary structure after simulation
bharat gupta
bharat.85.monu at gmail.com
Thu Jan 27 13:11:40 CET 2011
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 ..
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
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
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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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