Hi Justin Below is my nvt.mdp (nvt equilibration) file.i think probably you can have look at it and its not such big.
define = -DFLEXIBLE integrator = md nsteps = 50000 dt = 0.002 nstxout = 100 nstvout = 100 nstenergy = 100 nstlog = 100 constraint_algorithm = shake constraints = none unconstrained_start = yes shake_tol = 0.0001 morse = no ns_type = grid nstlist = 5 rlist = 1.0 coulombtype = PME rcoulomb = 1.0 vdwtype = Cut-off rvdw = 1.0 pme_order = 4 fourierspacing = 0.16 pbc = xyz tcoupl = V-rescale tc-grps = system tau_t = 0.1 ref_t = 300 DispCorr = Ener gen_vel = yes gen_temp = 300 gen_seed = 173529 regarding the plot i too know that one should use Xmgrace to plot. In the pressure Vs time(lysozyme tutorial) you have got two graphs. i to got the pressure Vs time (black line graph) my question is how to get the running average ( red line) and plot?. does i need any command to get the running average?. any help is highly appreciated. Regards Vinoth On Thu, Oct 21, 2010 at 4:56 PM, Justin A. Lemkul <jalem...@vt.edu> wrote: > > > vinothkumar mohanakrishnan wrote: > >> Hi justin >> >> I found what went wrong and i corrected my mdp file.now the system >> equilibrated to the desired temperature 300 K (plus r minus 30 K) is this >> ok? >> > > This is impossible to assess without seeing your .mdp settings. A > fluctuation of 10% is probably fine. > > > Apart from that i want to know how you plot the average running pressure >> and density in your tutorial for lyzosyme (redline). i just want to do that >> for DCE. any help is highly appreciated. >> >> > Xmgrace. > > -Justin > > Regards >> Vinoth >> >> >> On Wed, Oct 20, 2010 at 5:33 PM, Justin A. Lemkul <jalem...@vt.edu<mailto: >> jalem...@vt.edu>> wrote: >> >> >> >> vinothkumar mohanakrishnan wrote: >> >> Hi Justin >> >> I corrected the mistake what you said and i am able to run >> energy minimisation and equilibration. but when i view my em.gro >> and equilibration.gro in VMD it seems to me that the bonds >> between the atoms are broken in molecules.I used g_energy to >> check weather the system has >> >> >> VMD tries to guess where bonds should be, but does not always do a >> good job. Your topology defines bonds. These are the only bonds >> that there will be. None can be broken or formed in standard MD. >> >> >> equilibrated to the required temperature (300K) i found that the >> variation in the temperature was 100K (plus r minus) . i am not >> able find out what went wrong. any help is highly appreciated. >> >> >> Without seeing your .mdp file, there's no way to know. The >> fluctuation does seem too high, though, unless your system really is >> just that unstable. Are other properties converged - potential >> energy, density, etc? What type of ensemble are you using? >> >> -Justin >> >> Regards >> Vinoth >> >> >> On Mon, Oct 18, 2010 at 6:09 PM, Justin A. Lemkul >> <jalem...@vt.edu <mailto:jalem...@vt.edu> >> <mailto:jalem...@vt.edu <mailto:jalem...@vt.edu>>> wrote: >> >> >> >> vinothkumar mohanakrishnan wrote: >> >> Dear Justin >> >> what corrections i should make to ffoplsaan.itp to make it >> correct. what i should give instead of CAB and CLAA?. >> >> >> You must use atom types, not names. Unfortunately, you've >> chosen to >> use atom names, which are also types, which makes all of this >> quite >> confusing if you're not sure what you're doing. >> >> You defined two new atom types - opls_966 (CAB) and opls_967 >> (CLAA), >> which are the only indicators you are allowed to use if >> introducing >> new types. Thus, references to atom names (CAC, CLAD) will >> generate >> fatal errors. >> >> >> i copied the .rtp .atp .itp files from >> usr/local/gromacs/share/gromacs/top to my working >> directory and >> added these parameters to the corresponding files. what >> you mean >> is should i need to add these parameters to the source >> directory >> ( usr/local/gromacs/share/gromacs/top)? >> >> >> Your topology needs to be consistent with whatever files need >> to be >> included. By default, Gromacs checks the working directory >> first, >> but if you've moved to a new (sub)directory to carry out further >> steps, the grompp will not find your modified files, but will >> instead locate only the default force field files in $GMXLIB. >> Either keep all your work in one directory (which can get >> messy), >> or make use of the "include" keyword in the .mdp file. Any >> directory specified there will be searched after the working >> directory, but before $GMXLIB. >> >> -Justin >> >> Regards >> Vinoth >> >> >> On Mon, Oct 18, 2010 at 5:27 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: >> >> >> >> vinothkumar mohanakrishnan wrote: >> >> Hi all >> >> i added new atomtype for dichloroethane (DCE) and >> added the >> corresponding parameters in the .rtp, .atp, >> .bon.itp, .nb.itp >> respectively. given below are my additions to the >> corresponding >> files respectively. >> >> *ffoplsaa.rtp* >> >> [ DCE ] >> [ atoms ] >> CLAA opls_967 -0.2270 1 >> CAB opls_966 0.2270 1 >> CAC opls_966 0.2270 2 >> CLAD opls_967 -0.2270 2 >> >> [ bonds ] >> CLAA CAB >> CAB CAC >> CAC CLAD >> >> [ angles ] >> CLAA CAB CAC >> CAB CAC CLAD >> >> [ dihedrals ] >> CLAA CAB CAC CLAD >> >> *ffoplsaa.atp* >> >> opls_966 14.02700 ; CH2 for DCE >> opls_967 35.45300 ; CL for DCE >> >> *ffoplsaabon.itp* >> >> [bondtypes] >> CLAA CAB 1 0.17870 194137.6 ; CL-CH2 >> for DCE >> CAB CAC 1 0.15300 259408.0 ; CH2-CH2 >> for DCE >> CAC CLAD 1 0.17870 194137.6 ; CL-CH2 >> for DCE >> >> [angletypes] >> CLAA CAB CAC 1 108.200 368.192 ; >> C-C-CL >> for DCE >> CAB CAC CLAD 1 108.200 368.192 ; >> C-C-CL >> for DCE >> >> [dihedraltypes] >> CLAA CAB CAC CLAD 3 20.76096 >> -0.4184 27.011904 0.00000 0.00000 0.00000 >> ; for DCE >> >> >> You shouldn't be using atom names in the [*types] >> directives. >> What >> you should be using are the interpolated types from >> ffoplsaanb.itp, >> thus you have only utilized opls_966 (CAB) and >> opls_967 (CLAA). >> >> *ffoplsaanb.itp* >> >> >> opls_966 CAB 6 14.02700 0.227 A >> 3.98000e-01 >> 4.76976e-01 ; CH2 of DCE >> opls_967 CLAA 17 35.45300 -0.227 A >> 3.16000e-01 >> 0.20920e+01 ; Cl of DCE >> >> *dce.pdb* >> >> HETATM 1 CLAA DCE 1 6.300 -2.280 >> 1.360 1.00 >> 20.00 CL >> HETATM 2 CAB DCE 1 5.060 -3.540 >> 1.500 1.00 >> 20.00 C >> HETATM 3 CAC DCE 1 4.320 -3.740 >> 0.170 1.00 >> 20.00 C >> HETATM 4 CLAD DCE 1 3.270 -2.350 >> -0.210 1.00 >> 20.00 CL >> >> After adding all this, when i run grompp i get the >> error as >> *fatal error Unknown bond_atomtype CLAA*. can any >> one tell me >> why this happens?. >> >> >> Have you been sure to #include the correct (modified) >> force field >> files? That is, if you made a local copy and adjusted >> them, >> these >> won't be the files that pdb2gmx will #include by default. >> >> -Justin >> >> Regards >> Vinoth >> >> >> -- ======================================== >> >> 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 >> >> >> <mailto: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/Searchbefore >> 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>> >> <mailto: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 >> >> >> >> -- ======================================== >> >> 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 >> >> ======================================== >> -- 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 >> >> >> >> -- ======================================== >> >> 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 >> >> >> > -- > ======================================== > > 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 >
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