> 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 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 > > 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> 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>> 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 >>>> >>>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin >>>> >>>> ======================================== >>>> -- gmx-users mailing list gmx-users@gromacs.org >>>> <mailto:gmx-users@gromacs.org> >>>> <mailto: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> >>>> <mailto: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> >>>> <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> >>>> >>>> >>> >>> -- >>> 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 > >
-- 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
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