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

Thu, 27 Jan 2011 05:28:54 -0800 


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 <jalem...@vt.edu 
<mailto:jalem...@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.abra...@anu.edu.au <mailto:mark.abra...@anu.edu.au>
        <mailto:mark.abra...@anu.edu.au
        <mailto:mark.abra...@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
            <jalem...@vt.edu <mailto:jalem...@vt.edu>
               <mailto:jalem...@vt.edu <mailto:jalem...@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
                       <jalem...@vt.edu <mailto:jalem...@vt.edu>
            <mailto:jalem...@vt.edu <mailto:jalem...@vt.edu>>
                       <mailto:jalem...@vt.edu <mailto:jalem...@vt.edu>
            <mailto:jalem...@vt.edu <mailto:jalem...@vt.edu>>>> wrote:



                          Mark Abraham wrote:



                              On 01/27/11, *bharat gupta *
                       <bharat.85.m...@gmail.com
            <mailto:bharat.85.m...@gmail.com>
            <mailto:bharat.85.m...@gmail.com
            <mailto:bharat.85.m...@gmail.com>>
                              <mailto:bharat.85.m...@gmail.com
            <mailto:bharat.85.m...@gmail.com>
                       <mailto:bharat.85.m...@gmail.com
            <mailto:bharat.85.m...@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 : monu46...@yahoo.com
            <mailto:monu46...@yahoo.com>
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                          --     ========================================

                          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 : monu46...@yahoo.com
            <mailto:monu46...@yahoo.com> <mailto:monu46...@yahoo.com
            <mailto:monu46...@yahoo.com>>
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            <mailto:monu46...@yahoo.com> <mailto:monu46...@yahoo.com
            <mailto:monu46...@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 : monu46...@yahoo.com <mailto:monu46...@yahoo.com>
            <mailto:monu46...@yahoo.com <mailto:monu46...@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 : monu46...@yahoo.com <mailto:monu46...@yahoo.com>
        <mailto:monu46...@yahoo.com <mailto:monu46...@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 : monu46...@yahoo.com <mailto:monu46...@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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