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 .. On Thu, Jan 27, 2011 at 4:16 AM, Mark Abraham <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> 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>> wrote: >>> >>> >>> >>> Mark Abraham wrote: >>> >>> >>> >>> On 01/27/11, *bharat gupta * <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>> >>> >>> >>> >>> -- ======================================== >>> >>> 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 >>> >>> ======================================== >>> -- gmx-users mailing list gmx-users@gromacs.org >>> <mailto:gmx-users@gromacs.org> >>> >>> http://lists.gromacs.org/mailman/listinfo/gmx-users >>> Please search the archive at >>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting! >>> Please don't post (un)subscribe requests to the list. Use the www >>> interface or send it to gmx-users-requ...@gromacs.org >>> <mailto:gmx-users-requ...@gromacs.org>. >>> >>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >>> >>> >>> >>> >>> -- >>> 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 >> >> ======================================== >> -- >> gmx-users mailing list gmx-users@gromacs.org >> http://lists.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/Search before posting! >> Please don't post (un)subscribe requests to the list. Use the www >> interface or send it to gmx-users-requ...@gromacs.org. >> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> > > > > -- > 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 > > > > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- 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
-- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
