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

Justin A. Lemkul jalemkul at vt.edu
Thu Jan 27 14:27:36 CET 2011



bharat gupta wrote:
> I didn't gave any -c flag while md run .. and there is no confout.gro in 
> my folder .. I have attached the graph obtained after energy minimzation 

I've never heard of such a thing.  mdrun produces several files automatically: 
traj.trr, ener.edr, md.log, and confout.gro.  The output configuration is always 
written.  If it wasn't, then something is preventing mdrun from writing this 
file (full disk, read/write permissions, etc).

> .. I want to ask why the graph is not coming like the one shown in the 
> tutorial .. I guess I asked that same question earlier also ?? ..  Here 
> is the details of energy minimization result
>  

The shape of the graph is nearly identical.  You converged to an acceptable 
energy and force, so what's the problem?

If you're following the tutorial's procedure with a different system, there is 
absolutely no reason to expect that one system will converge to the same 
potential energy as another.  They're fundamentally different.  Even if you are 
working with the same system, there can be differences in the final energy.  EM 
is just a procedure to optimize the orientation of the molecules in the system. 
  It may converge somewhat differently each time you do it.

-Justin

> Steepest Descents converged to Fmax < 1000 in 720 steps
> Potential Energy  = -6.7970475e+05
> Maximum force     =  9.5201904e+02 on atom 78
> Norm of force     =  1.9553707e+01
>  
> 
> 
>  
> On Thu, Jan 27, 2011 at 5:12 AM, Justin A. Lemkul <jalemkul at vt.edu 
> <mailto:jalemkul at vt.edu>> wrote:
> 
> 
> 
>     bharat gupta wrote:
> 
>         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 ..
> 
> 
>     The structure after minimization (or any process done by mdrun) is
>     contained in whatever filename you passed to the -c flag.  If you
>     haven't specified any name, it is confout.gro.
> 
>     -Justin
> 
>         On Thu, Jan 27, 2011 at 4:16 AM, Mark Abraham
>         <Mark.Abraham at anu.edu.au <mailto:Mark.Abraham at anu.edu.au>
>         <mailto:Mark.Abraham at anu.edu.au
>         <mailto: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 <mailto:jalemkul at vt.edu>
>                <mailto: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>>
>                        <mailto: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>>
>                               <mailto: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>>>
>                                   <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
>             <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 <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
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>             <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/>
>             | (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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> 
>         -- 
>         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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