Re: [gmx-users] Force between groups
On 7/03/2010 4:24 PM, Michael McGovern wrote: Hi everyone. I have a trajectory file and for some analysis I'm doing I need to calcualte the force between two groups of atoms. Is there way to do this? Thank you. Set up an index file for your groups (see webpage), use those groups as energy groups (see manual) in a suitable .mdp file with nstfout>0 (see manual), apply grompp with the aforementioned two files, then mdrun -rerun on the old trajectory with the new .tpr. There is no way to decompose energies or forces after the fact, even if you used nstfout != 0 in the first place. This kind of procedure is exactly what mdrun -rerun is for. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] Force between groups
Hi everyone. I have a trajectory file and for some analysis I'm doing I need to calcualte the force between two groups of atoms. Is there way to do this? Thank you. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
SV: [gmx-users] Order parameter for unsaturated lipid chain in UAmodel
Sarah, I remember some changes to the double bond awhile back, perhaps you're using those? POPC (Berger/Tielman) is normally 'smoother' as Justin says. Maybe someone has a reference for the updates. Tim Sirk -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] Calculating Binding Affinity between Protein and Ligand using FEP
sunita gupta wrote: Hello all Earlier also I posted a query regarding FEP for protein ligand complex, but I dint not help much. Again I would like to share detailed information regarding the protocol I am following for calculation the binding free energy between protein and ligand using FEP(free energy perturbation) method. Please correct me if I am wrong anywhereas the values of *dVpot/dlambda dEkin/dlambda dG/dl constr *are continuously coming zero(0). I followed the gromacs tutorial of protien-ligand complex (http://cinjweb.umdnj.edu/~kerrigje/pdf_files/trp_drug_tutor.pdf) for preparing the coordinate and topology file for the whole system. For Free energy Calculation I followed the tutorial (http://www.dillgroup.ucsf.edu/group/wiki/index.php/Free_Energy:_Tutorial) for lambda value ranging from zero(0) to 1 and setup 11 independent job for each lambda value for 5 ns. But the* dVpot/dlambda dEkin/dlambda dG/dl constr* values in the *.log are continuously coming zero. Any help will be highly appreciated. What version of Gromacs are you using? If it's 3.3.x, you need to define a B-state for the molecule that you're trying to decouple. Furthermore, you should be decoupling charges and vdW parameters in separate steps; I believe that is mentioned in the tutorial material you quote above, and if not, it has surely been posted to this list several times. If you're using version 4.0.x, note that the free energy options have changed somewhat. Changes to the topology are not necessary, but different options must be set in the .mdp file. See the manual. -Justin For convenience I am also pasting my pro_constV.mdp (please let me know if any parameter is wrong of missing...which is leading to such problem) ; RUN CONTROL PARAMETERS = integrator = md ; start time and timestep in ps = tinit= 0 dt = 0.002 nsteps = 500 ; number of steps for center of mass motion removal = nstcomm = 100 ; OUTPUT CONTROL OPTIONS = ; Output frequency for coords (x), velocities (v) and forces (f) = nstxout = 5 nstvout = 5 nstfout = 0 ; Output frequency for energies to log file and energy file = nstlog = 500 nstenergy= 500 energygrps = protein non-protein ; Output frequency and precision for xtc file = nstxtcout= 5000 xtc-precision= 1000 ; This selects the subset of atoms for the xtc file. You can = ; select multiple groups. By default all atoms will be written. = ;xtc_grps = ; NEIGHBORSEARCHING PARAMETERS = ; nblist update frequency = nstlist = 10 ; ns algorithm (simple or grid) = ns_type = grid ; Periodic boundary conditions: xyz or none = ;pbc = xyz ; nblist cut-off = rlist= 1.0 ;domain-decomposition = no ; OPTIONS FOR ELECTROSTATICS AND VDW = ; Method for doing electrostatics = coulombtype = pme ;rcoulomb-switch = 0 rcoulomb = 1.0 ; Dielectric constant (DC) for cut-off or DC of reaction field = epsilon-r= 1 ; Method for doing Van der Waals = vdw-type = cut-off ; cut-off lengths= ;rvdw-switch = 0.8 rvdw = 1.4 ; Apply long range dispersion corrections for Energy and Pressure = DispCorr = EnerPres ; Spacing for the PME/PPPM FFT grid = fourierspacing = 0.1 ; FFT grid size, when a value is 0 fourierspacing will be used = fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 ; EWALD/PME/PPPM parameters = pme_order= 6 ewald_rtol = 1e-06 epsilon_surface = 0 optimize_fft = yes ;restraints ;dihre=yes ;dihre-fc=1 ;nstdihreout=1000 ;disre=simple ;disre_fc=1 ; Berendsen temperature coupling is on Tcoupl = berendsen tau_t = 0.1 0.1 tc_grps = protein non-protein ref_t = 300 300 ;OPTIONS FOR PRESSURE COUPLING Pcoupl = berendsen tau_p= 0.5 compressibility = 4.5e-05 ref_p= 1.0 ; Free energy control stuff free_energy = yes init_lambda = 0.0 delta_lambda = 0 sc_alpha = 0.5 sc-power = 1.0 sc-sigma = 0.3 ; GENERATE VELOCITIES FOR STARTUP RUN = gen_vel = yes gen_temp = 300 gen_seed = 173529 ; OPTIONS FOR BONDS = constraints = hbonds ; Type of constraint algorithm = constraint-algorithm = Lincs ; Do not constrain the start configuration = unconstrained-start = no ; Relative tolerance of shake = shake-tol= 0.0001 ; Highest order in the expansion of the constraint coupling matrix = lincs-order = 12 ; Lincs will write a wa
[gmx-users] Calculating Binding Affinity between Protein and Ligand using FEP
Hello all Earlier also I posted a query regarding FEP for protein ligand complex, but I dint not help much. Again I would like to share detailed information regarding the protocol I am following for calculation the binding free energy between protein and ligand using FEP(free energy perturbation) method. Please correct me if I am wrong anywhereas the values of *dVpot/dlambda dEkin/dlambda dG/dl constr *are continuously coming zero(0). I followed the gromacs tutorial of protien-ligand complex ( http://cinjweb.umdnj.edu/~kerrigje/pdf_files/trp_drug_tutor.pdf) for preparing the coordinate and topology file for the whole system. For Free energy Calculation I followed the tutorial ( http://www.dillgroup.ucsf.edu/group/wiki/index.php/Free_Energy:_Tutorial) for lambda value ranging from zero(0) to 1 and setup 11 independent job for each lambda value for 5 ns. But the* dVpot/dlambda dEkin/dlambda dG/dl constr* values in the *.log are continuously coming zero. Any help will be highly appreciated. For convenience I am also pasting my pro_constV.mdp (please let me know if any parameter is wrong of missing...which is leading to such problem) ; RUN CONTROL PARAMETERS = integrator = md ; start time and timestep in ps = tinit= 0 dt = 0.002 nsteps = 500 ; number of steps for center of mass motion removal = nstcomm = 100 ; OUTPUT CONTROL OPTIONS = ; Output frequency for coords (x), velocities (v) and forces (f) = nstxout = 5 nstvout = 5 nstfout = 0 ; Output frequency for energies to log file and energy file = nstlog = 500 nstenergy= 500 energygrps = protein non-protein ; Output frequency and precision for xtc file = nstxtcout= 5000 xtc-precision= 1000 ; This selects the subset of atoms for the xtc file. You can = ; select multiple groups. By default all atoms will be written. = ;xtc_grps = ; NEIGHBORSEARCHING PARAMETERS = ; nblist update frequency = nstlist = 10 ; ns algorithm (simple or grid) = ns_type = grid ; Periodic boundary conditions: xyz or none = ;pbc = xyz ; nblist cut-off = rlist= 1.0 ;domain-decomposition = no ; OPTIONS FOR ELECTROSTATICS AND VDW = ; Method for doing electrostatics = coulombtype = pme ;rcoulomb-switch = 0 rcoulomb = 1.0 ; Dielectric constant (DC) for cut-off or DC of reaction field = epsilon-r= 1 ; Method for doing Van der Waals = vdw-type = cut-off ; cut-off lengths= ;rvdw-switch = 0.8 rvdw = 1.4 ; Apply long range dispersion corrections for Energy and Pressure = DispCorr = EnerPres ; Spacing for the PME/PPPM FFT grid = fourierspacing = 0.1 ; FFT grid size, when a value is 0 fourierspacing will be used = fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 ; EWALD/PME/PPPM parameters = pme_order= 6 ewald_rtol = 1e-06 epsilon_surface = 0 optimize_fft = yes ;restraints ;dihre=yes ;dihre-fc=1 ;nstdihreout=1000 ;disre=simple ;disre_fc=1 ; Berendsen temperature coupling is on Tcoupl = berendsen tau_t = 0.1 0.1 tc_grps = protein non-protein ref_t = 300 300 ;OPTIONS FOR PRESSURE COUPLING Pcoupl = berendsen tau_p= 0.5 compressibility = 4.5e-05 ref_p= 1.0 ; Free energy control stuff free_energy = yes init_lambda = 0.0 delta_lambda = 0 sc_alpha = 0.5 sc-power = 1.0 sc-sigma = 0.3 ; GENERATE VELOCITIES FOR STARTUP RUN = gen_vel = yes gen_temp = 300 gen_seed = 173529 ; OPTIONS FOR BONDS = constraints = hbonds ; Type of constraint algorithm = constraint-algorithm = Lincs ; Do not constrain the start configuration = unconstrained-start = no ; Relative tolerance of shake = shake-tol= 0.0001 ; Highest order in the expansion of the constraint coupling matrix = lincs-order = 12 ; Lincs will write a warning to the stderr if in one step a bond = ; rotates over more degrees than = lincs-warnangle = 30 -- Best Regards SUNITA GUPTA Member Research Team LeadInvent Technology TBIU, IIT Delhi, India Email- sun...@leadinvent.com Ph- +9111 26581524 (Ex-6) -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_l
