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 ..
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
rmsd_(1).pdf
Description: Adobe PDF document
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