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>> 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>> 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>>> 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>>> 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> <mailto:monu46...@yahoo.com
            <mailto:monu46...@yahoo.com>>
                       <mailto: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/> <http://vt.edu
            <http://vt.edu/>> | (540) 231-9080

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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>



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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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