[gmx-users] Re: change in the secondary structure after simulation
Mark Abraham
Mark.Abraham at anu.edu.au
Thu Jan 27 13:16:58 CET 2011
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
> <mailto: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>
> <mailto: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>
> <mailto: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>>
> <mailto: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/> <http://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>
> <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>
>
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