[gmx-users] phi/psi
Hi, How to get phi/psi angles from gromacs trajectory file? I used v.4.5.5. best Urszula Urszula Uciechowska PhD University of Gdansk and Medical Univesity of Gdansk Department of Molecular and Cellular Biology ul. Abrahama 58 80-307 Gdańsk Poland - Ta wiadomość została wysłana z serwera Uniwersytetu Gdańskiego http://www.ug.edu.pl/ -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] REMD implicit solvent
Hi, I should run it by using mdrun_mpi? best Urszula > Hello, > > From my experience, the domain decomposition is not compatible with > implicit solvent, you have to switch > to particle decomposition for the simulations. > > > All the best, > Qinghua > > On 01/05/2018 12:40 PM, Urszula Uciechowska wrote: >> Hi, >> >> I just run a normal single-replica. Now the error that I have is: >> >> Program mdrun_mpi, VERSION 4.5.5 >> Source code file: domdec.c, line: 3266 >> >> Software inconsistency error: >> Inconsistent DD boundary staggering limits! >> For more information and tips for troubleshooting, please check the >> GROMACS >> website at http://www.gromacs.org/Documentation/Errors >> >> >> Any suggestions? What can I do to run it? >> >> Thanks >> Ula >> >>> Hi, >>> >>> Did you try to debug your setup by running a normal single-replica >>> simulation first? >>> >>> Mark >>> >>> On Fri, Jan 5, 2018 at 12:12 PM Urszula Uciechowska < >>> urszula.uciechow...@biotech.ug.edu.pl> wrote: >>> >>>> >>>> Dear gromacs users, >>>> >>>> I am trying to run REMD simulations using 4.5.5 version (implicit >>>> solvent). The MD procedure: >>>> >>>> pdb2gmx -f prot.pdb -o prot.gro -q prot.pdb -ignh -ss. >>>> >>>> The input for minimization step: >>>> >>>> ; Run control parameters >>>> integrator = cg >>>> nsteps = 800 >>>> vdwtype = cut-off >>>> coulombtype = cut-off >>>> ;cutoff-scheme= group >>>> pbc = no >>>> periodic_molecules = no >>>> nstlist = 10 >>>> ns_type = grid >>>> rlist= 1.0 >>>> rcoulomb = 1.6 >>>> rvdw = 1.6 >>>> comm-mode= Angular >>>> nstcomm = 10 >>>> ; >>>> ;Energy minimizing stuff >>>> ; >>>> emtol= 100.0 >>>> nstcgsteep = 2 >>>> emstep = 0.01 >>>> ; >>>> ;Relative dielectric constant for the medium and the reaction field >>>> epsilon_r= 1 >>>> epsilon_rf = 1 >>>> ; >>>> ; Implicit solvent >>>> ; >>>> implicit_solvent = GBSA >>>> gb_algorithm = OBC ;Still HCT OBC >>>> nstgbradii = 1.0 >>>> rgbradii = 1.0 ; [nm] Cut-off for the calculation >>>> of >>>> the Born radii. Currently must be equal to rlist >>>> gb_epsilon_solvent = 80 ; Dielectric constant for the >>>> implicit >>>> solvent >>>> gb_saltconc = 0; Salt concentration for implicit >>>> solvent models, currently not used >>>> sa_algorithm = Ace-approximation >>>> sa_surface_tension = 2.05016 ; Surface tension (kJ/mol/nm^2) >>>> for >>>> the SA (nonpolar surface) part of GBSA. The value -1 will set default >>>> value for Still/HCT/OBC GB-models. >>>> >>>> and it finished without errors. >>>> >>>> The problem is with equilibration step. The input file that I used is: >>>> >>>> ; MD CONTROL OPTIONS >>>> integrator = md >>>> dt = 0.002 >>>> nsteps = 5 ; 10 ns >>>> init_step = 0; For exact run continuation or >>>> redoing part of a run >>>> comm-mode = Angular ; mode for center of mass >>>> motion >>>> removal >>>> nstcomm = 10 ; number of steps for center of >>>> mass motion removal >>>> >>>> ; OUTPUT CONTROL OPTIONS >>>> ; Output frequency for coords (x), velocities (v) and forces (f) >>>> nstxout = 1000 >>>> nstvout = 1000 >>>> nstfout = 1000 >>>> >>>> ; Output frequency for energies to log file and energy file >>>> nstlog = 1000 >>>> nstcalcenergy= 10 >>>> nstenergy= 1000
Re: [gmx-users] REMD implicit solvent
Hi, I just run a normal single-replica. Now the error that I have is: Program mdrun_mpi, VERSION 4.5.5 Source code file: domdec.c, line: 3266 Software inconsistency error: Inconsistent DD boundary staggering limits! For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors Any suggestions? What can I do to run it? Thanks Ula > Hi, > > Did you try to debug your setup by running a normal single-replica > simulation first? > > Mark > > On Fri, Jan 5, 2018 at 12:12 PM Urszula Uciechowska < > urszula.uciechow...@biotech.ug.edu.pl> wrote: > >> >> >> Dear gromacs users, >> >> I am trying to run REMD simulations using 4.5.5 version (implicit >> solvent). The MD procedure: >> >> pdb2gmx -f prot.pdb -o prot.gro -q prot.pdb -ignh -ss. >> >> The input for minimization step: >> >> ; Run control parameters >> integrator = cg >> nsteps = 800 >> vdwtype = cut-off >> coulombtype = cut-off >> ;cutoff-scheme= group >> pbc = no >> periodic_molecules = no >> nstlist = 10 >> ns_type = grid >> rlist= 1.0 >> rcoulomb = 1.6 >> rvdw = 1.6 >> comm-mode= Angular >> nstcomm = 10 >> ; >> ;Energy minimizing stuff >> ; >> emtol= 100.0 >> nstcgsteep = 2 >> emstep = 0.01 >> ; >> ;Relative dielectric constant for the medium and the reaction field >> epsilon_r= 1 >> epsilon_rf = 1 >> ; >> ; Implicit solvent >> ; >> implicit_solvent = GBSA >> gb_algorithm = OBC ;Still HCT OBC >> nstgbradii = 1.0 >> rgbradii = 1.0 ; [nm] Cut-off for the calculation >> of >> the Born radii. Currently must be equal to rlist >> gb_epsilon_solvent = 80 ; Dielectric constant for the >> implicit >> solvent >> gb_saltconc = 0; Salt concentration for implicit >> solvent models, currently not used >> sa_algorithm = Ace-approximation >> sa_surface_tension = 2.05016 ; Surface tension (kJ/mol/nm^2) for >> the SA (nonpolar surface) part of GBSA. The value -1 will set default >> value for Still/HCT/OBC GB-models. >> >> and it finished without errors. >> >> The problem is with equilibration step. The input file that I used is: >> >> ; MD CONTROL OPTIONS >> integrator = md >> dt = 0.002 >> nsteps = 5 ; 10 ns >> init_step = 0; For exact run continuation or >> redoing part of a run >> comm-mode = Angular ; mode for center of mass motion >> removal >> nstcomm = 10 ; number of steps for center of >> mass motion removal >> >> ; OUTPUT CONTROL OPTIONS >> ; Output frequency for coords (x), velocities (v) and forces (f) >> nstxout = 1000 >> nstvout = 1000 >> nstfout = 1000 >> >> ; Output frequency for energies to log file and energy file >> nstlog = 1000 >> nstcalcenergy= 10 >> nstenergy= 1000 >> >> ; Neighbor searching and Electrostatitcs >> vdwtype = cut-off >> coulombtype = cut-off >> ;cutoff-scheme= group >> pbc = no >> periodic_molecules = no >> nstlist = 5 >> ns_type = grid >> rlist= 1.0 >> rcoulomb = 1.6 >> rvdw = 1.0 >> ; Selection of energy groups >> energygrps = fixed not_fixed >> freezegrps = fixed not_fixed >> freezedim= Y Y Y N N N >> >> ;Relative dielectric constant for the medium and the reaction field >> epsilon_r= 1 >> epsilon_rf = 1 >> >> ; Temperutare coupling >> tcoupl = v-rescale >> tc_grps = fixed not_fixed >> tau_t= 0.01 0.01 >> ;nst_couple = 5 >> ref_t= 300.00 300.00 >> >> ; Pressure coupling >> pcoupl = no >> ;pcoupletype = isotropic >> tau_p= 1.0 >> ;compressiblity = 4.
[gmx-users] REMD implicit solvent
Dear gromacs users, I am trying to run REMD simulations using 4.5.5 version (implicit solvent). The MD procedure: pdb2gmx -f prot.pdb -o prot.gro -q prot.pdb -ignh -ss. The input for minimization step: ; Run control parameters integrator = cg nsteps = 800 vdwtype = cut-off coulombtype = cut-off ;cutoff-scheme= group pbc = no periodic_molecules = no nstlist = 10 ns_type = grid rlist= 1.0 rcoulomb = 1.6 rvdw = 1.6 comm-mode= Angular nstcomm = 10 ; ;Energy minimizing stuff ; emtol= 100.0 nstcgsteep = 2 emstep = 0.01 ; ;Relative dielectric constant for the medium and the reaction field epsilon_r= 1 epsilon_rf = 1 ; ; Implicit solvent ; implicit_solvent = GBSA gb_algorithm = OBC ;Still HCT OBC nstgbradii = 1.0 rgbradii = 1.0 ; [nm] Cut-off for the calculation of the Born radii. Currently must be equal to rlist gb_epsilon_solvent = 80 ; Dielectric constant for the implicit solvent gb_saltconc = 0; Salt concentration for implicit solvent models, currently not used sa_algorithm = Ace-approximation sa_surface_tension = 2.05016 ; Surface tension (kJ/mol/nm^2) for the SA (nonpolar surface) part of GBSA. The value -1 will set default value for Still/HCT/OBC GB-models. and it finished without errors. The problem is with equilibration step. The input file that I used is: ; MD CONTROL OPTIONS integrator = md dt = 0.002 nsteps = 5 ; 10 ns init_step = 0; For exact run continuation or redoing part of a run comm-mode = Angular ; mode for center of mass motion removal nstcomm = 10 ; number of steps for center of mass motion removal ; OUTPUT CONTROL OPTIONS ; Output frequency for coords (x), velocities (v) and forces (f) nstxout = 1000 nstvout = 1000 nstfout = 1000 ; Output frequency for energies to log file and energy file nstlog = 1000 nstcalcenergy= 10 nstenergy= 1000 ; Neighbor searching and Electrostatitcs vdwtype = cut-off coulombtype = cut-off ;cutoff-scheme= group pbc = no periodic_molecules = no nstlist = 5 ns_type = grid rlist= 1.0 rcoulomb = 1.6 rvdw = 1.0 ; Selection of energy groups energygrps = fixed not_fixed freezegrps = fixed not_fixed freezedim= Y Y Y N N N ;Relative dielectric constant for the medium and the reaction field epsilon_r= 1 epsilon_rf = 1 ; Temperutare coupling tcoupl = v-rescale tc_grps = fixed not_fixed tau_t= 0.01 0.01 ;nst_couple = 5 ref_t= 300.00 300.00 ; Pressure coupling pcoupl = no ;pcoupletype = isotropic tau_p= 1.0 ;compressiblity = 4.5e-5 ref_p= 1.0 gen_vel = yes gen_temp = 300.00 300.00 gen_seed = -1 constraints = h-bonds ; Implicit solvent implicit_solvent = GBSA gb_algorithm = Still ; HCT ; OBC nstgbradii = 1.0 rgbradii = 1.0 ; [nm] Cut-off for the calculation of the Born radii. Currently must be equal to rlist gb_epsilon_solvent = 80 ; Dielectric constant for the implicit solvent gb_saltconc = 0; Salt concentration for implicit solvent models, currently not used sa_algorithm = Ace-approximation sa_surface_tension = 2.05016 ; Surface tension (kJ/mol/nm^2) for the SA (nonpolar surface) part of GBSA. The value -1 will set default value for Still/HCT/OBC GB-models. mdrun -v -multidir eq_[12345678] The error that I obtained is: Fatal error: A charge group moved too far between two domain decomposition steps This usually means that your system is not well equilibrated For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors I do not know what is wrong. I checked the Fatal error at www.gromacs.org/Documentation/Errors. My system is ok, I tried to increase the min steps but did not help. I have also checked the http://www.gromacs.org/Documentation/How-tos/REMD but can not move forward because of equilibration step. I appreciate any recommendation. Thanks Urszula Urszula Uciechowska PhD University of Gdansk and Medical Univesity of Gdansk
[gmx-users] chainsep in pdb2gmx
Dear gmx users, I am trying to prepare a protein-dimer DNA complex for MD. The problem is that after running pdb2gmx some of the chains are joined. How to use chainsep to separate for example chain A and chain B. In my pdb file chains are separated by TER flag but it still does not work. thanks for any advice best Ula Urszula Uciechowska PhD University of Gdansk and Medical Univesity of Gdansk Department of Molecular and Cellular Biology ul. Abrahama 58 80-307 Gdańsk Poland - Ta wiadomość została wysłana z serwera Uniwersytetu Gdańskiego http://www.ug.edu.pl/ -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] fatal error
Hi, I do not know. After running pdb2gmx I am not getting the .itp file for the DC5... I am using gromacs 5.0.4. What can be wrong here? Urszula > Hi, > > What name does the .rtp entry for DC5 use for its phosphorus atom? > > Mark > > On Mon, Mar 6, 2017 at 1:39 PM Urszula Uciechowska < > urszula.uciechow...@biotech.ug.edu.pl> wrote: > >> Dear gmx users, >> >> After running a pdb2gmx script of the pdb file I am getting an error >> message: >> >> >> Fatal error: >> Atom P in residue DC 2 was not found in rtp entry DC5 with 28 atoms >> while sorting atoms. >> >> >> The DC 2 in pdb file: >> >> TER 11412 LEU B 366 >> ATOM 11413 P DC C 2 0.997 17.702 5.368 1.00 77.21 >> P >> ATOM 11414 OP1 DC C 2 -0.278 17.623 4.612 1.00 76.82 >> O >> ATOM 11415 OP2 DC C 2 1.374 16.596 6.287 1.00 76.77 >> O >> ATOM 11416 O5' DC C 2 2.181 17.899 4.319 1.00 75.66 >> O >> ATOM 11417 C5' DC C 2 2.302 19.107 3.565 1.00 72.46 >> C >> >> What can be wrong with the P atom? >> >> Thanks for any suggestions. >> >> best >> Urszula Uciechowska >> >> >> >> >> - >> Ta wiadomość została wysłana z serwera Uniwersytetu Gdańskiego >> http://www.ug.edu.pl/ >> >> -- >> Gromacs Users mailing list >> >> * Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before >> posting! >> >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> >> * For (un)subscribe requests visit >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >> send a mail to gmx-users-requ...@gromacs.org. > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send > a mail to gmx-users-requ...@gromacs.org. Urszula Uciechowska PhD University of Gdansk and Medical Univesity of Gdansk Department of Molecular and Cellular Biology ul. Abrahama 58 80-307 Gdańsk Poland - Ta wiadomość została wysłana z serwera Uniwersytetu Gdańskiego http://www.ug.edu.pl/ -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] fatal error
Dear gmx users, After running a pdb2gmx script of the pdb file I am getting an error message: Fatal error: Atom P in residue DC 2 was not found in rtp entry DC5 with 28 atoms while sorting atoms. The DC 2 in pdb file: TER 11412 LEU B 366 ATOM 11413 P DC C 2 0.997 17.702 5.368 1.00 77.21 P ATOM 11414 OP1 DC C 2 -0.278 17.623 4.612 1.00 76.82 O ATOM 11415 OP2 DC C 2 1.374 16.596 6.287 1.00 76.77 O ATOM 11416 O5' DC C 2 2.181 17.899 4.319 1.00 75.66 O ATOM 11417 C5' DC C 2 2.302 19.107 3.565 1.00 72.46 C What can be wrong with the P atom? Thanks for any suggestions. best Urszula Uciechowska - Ta wiadomość została wysłana z serwera Uniwersytetu Gdańskiego http://www.ug.edu.pl/ -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] input file
Dear gmx users, I am using 5.0.6 version. After running the: grompp -f ions.mdp -c caulob-mod-it_solvated.gro -p caulob-mod-it.top -o ions.tpr NOTE 1 [file ions.mdp, line 16]: ions.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it was first intended for use with GROMACS before 4.6. In 4.6, the Verlet scheme was introduced, but the group scheme was still the default. The default is now the Verlet scheme, so you will observe different behaviour. What should I apply in cutoff-scheme ? Please see below my input.file ions.mpd contains: ; ions.mdp - used as input into grompp to generate ions.tpr ; Parameters describing what to do, when to stop and what to save integrator = steep ; Algorithm (steep = steepest descent minimization) emtol = 1000.0; Stop minimization when the maximum force < 1000.0 kJ/mol/nm emstep = 0.01 ; Energy step size nsteps = 5 ; Maximum number of (minimization) steps to perform ; Parameters describing how to find the neighbors of each atom and how to calculate the interactions nstlist = 10; Frequency to update the neighbor list and long range forces ns_type = grid ; Method to determine neighbor list (simple, grid) rlist = 1.0 ; Cut-off for making neighbor list (short range forces) coulombtype = PME ; Treatment of long range electrostatic interactions rcoulomb= 1.0 ; Short-range electrostatic cut-off rvdw= 1.0 ; Short-range Van der Waals cut-off pbc = xyz ; Periodic Boundary Conditions (yes/no) best Urszula University of Gdansk and Medical Univesity of Gdansk Department of Molecular and Cellular Biology ul. Kladki 24 80-822 Gdansk Poland - Ta wiadomość została wysłana z serwera Uniwersytetu Gdańskiego http://www.ug.edu.pl/ -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] tutorial
Dear all, I am trying to follow the tutorial: http://nmr.chem.uu.nl/~adrien/course/molmod/analysis2.html Part: ANALYSIS OF DYNAMICS AND TIME-AVERAGED PROPERTIES In the command: trjconv -f traj_helix.xtc -o traj_helix_10-50ns.xtc -n _peptide_index.ndx -pbc nojump -dt 100 -b 1 what is the traj_helix.xtc? Thank you in advance for your help. best regards Urszula Uciechowska University of Gdansk and Medical Univesity of Gdansk Department of Molecular and Cellular Biology ul. Kladki 24 80-822 Gdansk Poland - Ta wiadomość została wysłana z serwera Uniwersytetu Gdańskiego http://www.ug.edu.pl/ -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] tutorial
Dear all, I am trying to follow the tutorial: http://nmr.chem.uu.nl/~adrien/course/molmod/analysis2.html Part: ANALYSIS OF DYNAMICS AND TIME-AVERAGED PROPERTIES In the command: trjconv -f traj_helix.xtc -o traj_helix_10-50ns.xtc -n _peptide_index.ndx -pbc nojump -dt 100 -b 1 what is the traj_helix.xtc? Thank you in advance for your help. best regards Urszula Uciechowska University of Gdansk and Medical Univesity of Gdansk Department of Molecular and Cellular Biology ul. Kladki 24 80-822 Gdansk Poland - Ta wiadomość została wysłana z serwera Uniwersytetu Gdańskiego http://www.ug.edu.pl/ -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] GMXPBSA
Dear gromacs users, I would like to run BFE calculations with gromacs. I performed MD simulations for 100ns and would like to extract snapshots from the MD and split them into the complex, protein and DNA. My question is how many sps should I extarct from the MD? and Are there any scripts available for this step? Thanks for any suggestions best regards Urszula University of Gdansk and Medical Univesity of Gdansk Department of Molecular and Cellular Biology ul. Kladki 24 80-822 Gdansk Poland - Ta wiadomość została wysłana z serwera Uniwersytetu Gdańskiego http://www.ug.edu.pl/ -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] error gcq#360
Dear gmx users, after running grompp -f em.mdp -c COM_ions.gro -p COM.top -o em.tpr I obtained: GROMACS: gmx grompp, VERSION 5.0 Executable: /software/local/el6/INTEL/gromacs/5.0.0/intel-ompi-fftw-blas-lapack/bin/gmx Library dir: /software/local/el6/INTEL/gromacs/5.0.0/intel-ompi-fftw-blas-lapack/share/gromacs/top Command line: grompp -f em.mdp -c COM_ions.gro -p COM.top -o em.tpr Back Off! I just backed up mdout.mdp to ./#mdout.mdp.3# Setting the LD random seed to 2993272762 Generated 2211 of the 2211 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 2211 of the 2211 1-4 parameter combinations Excluding 3 bonded neighbours molecule type 'DNA' Excluding 3 bonded neighbours molecule type 'DNA2' Excluding 3 bonded neighbours molecule type 'Protein3' Excluding 3 bonded neighbours molecule type 'Protein4' Excluding 3 bonded neighbours molecule type 'Protein5' Excluding 3 bonded neighbours molecule type 'Protein6' Excluding 2 bonded neighbours molecule type 'SOL' Excluding 1 bonded neighbours molecule type 'NA' Excluding 1 bonded neighbours molecule type 'CL' Removing all charge groups because cutoff-scheme=Verlet Analysing residue names: There are: 136DNA residues There are: 1140Protein residues There are: 557197 Water residues There are: 2152Ion residues Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... Analysing Protein... Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... Number of degrees of freedom in T-Coupling group rest is 5090256.00 Calculating fourier grid dimensions for X Y Z Using a fourier grid of 216x216x216, spacing 0.119 0.119 0.119 Estimate for the relative computational load of the PME mesh part: 0.27 NOTE 1 [file em.mdp]: This run will generate roughly 586540 Mb of data There was 1 note gcq#360: error: too many template-parameter-lists (g++) At the end I have em.tpr file but I am not sure if everything is ok. Any suggestions. best regards Urszula - Ta wiadomość została wysłana z serwera Uniwersytetu Gdańskiego http://www.ug.edu.pl/ -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] How to run pdb2gmx with -ter flag?
Hi, Now I have GROMACS v 5.0. What option should I select for -chainsep? -chainsep enum (id_or_ter) Condition in PDB files when a new chain should be started (adding termini): id_or_ter, id_and_ter, ter, id, interactive Should I change something in my PDB file? This is not clear for me. Thank you for your help Urszula Hi, -ter does not solve this problem. You should not start new work with such an old version of GROMACS; I forget when we added -chainsep, but it solves this problem. Mark On Wed, 6 May 2015 15:37 Urszula Uciechowska urszula.uciechow...@biotech.ug.edu.pl wrote: Hi, I have problems with using -tar flag in pdb2gmx, after running pdb2gmx -f COM-oH.pdb -o COM-oH.gro -p COM-oH.top -ter -ignh -water tip3p I do not get any errors however after generating a pdb using editconf I am getting a complex where the receptors are connected with bonds. What I am doing wrong? I have also tried to put the ter cards in my pdb (COM-oH.pdb): ATOM 2779 O2 DC3 136 96.011 58.127 145.405 1.00 0.00 O ATOM 2780 C3' DC3 136 94.583 61.640 142.148 1.00 0.00 C ATOM 2781 C2' DC3 136 95.682 60.578 142.176 1.00 0.00 C ATOM 2782 O3' DC3 136 94.914 62.682 143.055 1.00 0.00 O ter ATOM 2784 N MET 137 -55.937 52.177 172.707 1.00 0.00 N ATOM 2785 CA MET 137 -57.391 52.043 172.937 1.00 0.00 C ATOM 2786 CB MET 137 -58.028 53.416 173.205 1.00 0.00 C but after running pdb2gmx I am getting an error message: --- Program pdb2gmx, VERSION 4.5.3 Source code file: pdb2gmx.c, line: 655 Fatal error: Atom OXT in residue ARG 421 was not found in rtp entry ARG with 24 atoms while sorting atoms. . For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- How to run it correctly? Urszula Uciechowska University of Gdansk and Medical Univesity of Gdansk Department of Molecular and Cellular Biology ul. Kladki 24 80-822 Gdansk Poland - Ta wiadomość została wysłana z serwera Uniwersytetu Gdańskiego http://www.ug.edu.pl/ -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. University of Gdansk and Medical Univesity of Gdansk Department of Molecular and Cellular Biology ul. Kladki 24 80-822 Gdansk Poland - Ta wiadomość została wysłana z serwera Uniwersytetu Gdańskiego http://www.ug.edu.pl/ -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Fatal error
Hi, I am trying to run pdb2gmx by using: pdb2gmx -f COM-oH.pdb -o COM-oH.gro -p COM-oH.top -ignh -water tip3p -ter however I am getting a fatal error: --- Program pdb2gmx, VERSION 4.5.3 Source code file: pgutil.c, line: 99 Fatal error: Atom C not found in residue seq.nr. 137 while adding atom For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- (That makes 100 errors; please try again.) (TeX) I have checkec the 137 AA and there is C atom. The system consist of DNA and 3 protein receptors. I used 6: AMBER99SB-ILDN force field. What is wrong here? best regards Urszula University of Gdansk and Medical Univesity of Gdansk Department of Molecular and Cellular Biology ul. Kladki 24 80-822 Gdansk Poland - Ta wiadomość została wysłana z serwera Uniwersytetu Gdańskiego http://www.ug.edu.pl/ -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] How to run pdb2gmx with -ter flag?
Hi, I have problems with using -tar flag in pdb2gmx, after running pdb2gmx -f COM-oH.pdb -o COM-oH.gro -p COM-oH.top -ter -ignh -water tip3p I do not get any errors however after generating a pdb using editconf I am getting a complex where the receptors are connected with bonds. What I am doing wrong? I have also tried to put the ter cards in my pdb (COM-oH.pdb): ATOM 2779 O2 DC3 136 96.011 58.127 145.405 1.00 0.00 O ATOM 2780 C3' DC3 136 94.583 61.640 142.148 1.00 0.00 C ATOM 2781 C2' DC3 136 95.682 60.578 142.176 1.00 0.00 C ATOM 2782 O3' DC3 136 94.914 62.682 143.055 1.00 0.00 O ter ATOM 2784 N MET 137 -55.937 52.177 172.707 1.00 0.00 N ATOM 2785 CA MET 137 -57.391 52.043 172.937 1.00 0.00 C ATOM 2786 CB MET 137 -58.028 53.416 173.205 1.00 0.00 C but after running pdb2gmx I am getting an error message: --- Program pdb2gmx, VERSION 4.5.3 Source code file: pdb2gmx.c, line: 655 Fatal error: Atom OXT in residue ARG 421 was not found in rtp entry ARG with 24 atoms while sorting atoms. . For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- How to run it correctly? Urszula Uciechowska University of Gdansk and Medical Univesity of Gdansk Department of Molecular and Cellular Biology ul. Kladki 24 80-822 Gdansk Poland - Ta wiadomość została wysłana z serwera Uniwersytetu Gdańskiego http://www.ug.edu.pl/ -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] DNA-protein complex
The force field that I used was ambe99bsc0, and my input file was: ; 7.3.3 Run Control integrator = md; md integrator tinit = 0 ; [ps] starting time for run dt = 0.002 ; [ps] time step for integration nsteps = 500 ; maximum number of steps to integrate, 0.002 * 2,500,000 = 5,000 ps comm_mode = Linear; remove center of mass translation nstcomm = 1 ; [steps] frequency of mass motion removal comm_grps = Protein Non-Protein ; group(s) for center of mass motion removal ; 7.3.8 Output Control nstxout = 250 ; [steps] freq to write coordinates to trajectory nstvout = 250 ; [steps] freq to write velocities to trajectory nstfout = 250 ; [steps] freq to write forces to trajectory nstlog = 100 ; [steps] freq to write energies to log file nstenergy = 500 ; [steps] freq to write energies to energy file nstxtcout = 500 ; [steps] freq to write coordinates to xtc trajectory xtc_precision = 1000 ; [real] precision to write xtc trajectory xtc_grps= System; group(s) to write to xtc trajectory energygrps = System; group(s) to write to energy file ; 7.3.9 Neighbor Searching nstlist = 1 ; [steps] freq to update neighbor list ns_type = grid ; method of updating neighbor list pbc = xyz ; periodic boundary conditions in all directions rlist = 0.8 ; [nm] cut-off distance for the short-range neighbor list ; 7.3.10 Electrostatics coulombtype = PME ; Particle-Mesh Ewald electrostatics rcoulomb= 0.8 ; [nm] distance for Coulomb cut-off ; 7.3.11 VdW vdwtype = cut-off ; twin-range cut-off with rlist where rvdw = rlist rvdw= 0.8 ; [nm] distance for LJ cut-off DispCorr= EnerPres ; apply long range dispersion corrections for energy ; 7.3.13 Ewald fourierspacing = 0.12 ; [nm] grid spacing for FFT grid when using PME pme_order = 4 ; interpolation order for PME, 4 = cubic ewald_rtol = 1e-5 ; relative strength of Ewald-shifted potential at rcoulomb ; 7.3.14 Temperature Coupling tcoupl = v-rescale ; temperature coupling with Nose-Hoover ensemble tc_grps = ProteinNon-Protein; groups to couple seperately to temperature bath tau_t = 0.10.1; [ps] time constant for coupling ref_t = 310310; [K] reference temperature for coupling ; 7.3.15 Pressure Coupling pcoupl = parrinello-rahman ; pressure coupling where box vectors are variable pcoupltype = isotropic ; pressure coupling in x-y-z directions tau_p = 2.0 ; [ps] time constant for coupling compressibility = 4.5e-5; [bar^-1] compressibility ref_p = 1.0 ; [bar] reference pressure for coupling ; 7.3.17 Velocity Generation gen_vel = no; velocity generation turned off ; 7.3.18 Bonds constraints = all-bonds ; convert all bonds to constraints constraint_algorithm= LINCS ; LINear Constraint Solver continuation= yes ; apply constraints to the start configuration lincs_order = 4 ; highest order in the expansion of the contraint coupling matrix lincs_iter = 1 ; number of iterations to correct for rotational lengthening lincs_warnangle = 30; [degrees] maximum angle that a bond can rotate before LINCS will complain best regards Urszula Uciechowska 2015-03-17 14:35 GMT-03:00 Urszula Uciechowska urszula.uciechow...@biotech.ug.edu.pl: Hi, I am running MD for dsDNA-protein complex. After 50ns I observed that the DNA is unwinding. What did go wrong? Should I have changed something in my input file? You might want to send your input files, so as your force field that you have choose. It is hard to say anything without more details. Also, what do you mean by 'unwinding'? Could you be more specific? Thank you in advance for your suggestions. best regards Urszula Cheers! -- Marcelo Depólo Polêto B.Sc. Biochemistry - University of Viçosa (Brazil) -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org
[gmx-users] DNA-protein complex
Hi, I am running MD for dsDNA-protein complex. After 50ns I observed that the DNA is unwinding. What did go wrong? Should I have changed something in my input file? Thank you in advance for your suggestions. best regards Urszula - Ta wiadomość została wysłana z serwera Uniwersytetu Gdańskiego http://www.ug.edu.pl/ -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] dihedral angle g_angle?
HI I use mk_angndx to produce angle.ndx then, I entered g_angle -od angdist.xvg -ov angaver.xvg -type dihedral it follows the options: Group 0 ( Phi=0.0_3_0.60) has 368 elements Group 1 ( Phi=0.0_2_4.92) has 368 elements Group 2 ( Phi=0.0_3_0.65) has 1104 elements Group 3 ( Phi=0.0_3_1.60) has 736 elements Group 4 (Phi=180.0_2_0.42) has 552 elements Group 5 ( Phi=0.0_3_1.60) has 528 elements Group 6 ( Phi=0.0_3_0.75) has 368 elements Group 7 (Phi=180.0_2_1.05) has 368 elements Group 8 (Phi=180.0_1_0.84) has 368 elements Group 9 ( Phi=0.0_2_2.72) has 184 elements Group10 (Phi=0.0_1_10.46) has 184 elements Group11 ( Phi=0.0_0_0.00) has 552 elements Group12 (Phi=180.0_2_7.11) has 184 elements Group13 (Phi=180.0_2_6.90) has 368 elements Group14 (Phi=180.0_2_41.84) has92 elements Group15 (Phi=180.0_2_10.67) has 288 elements Group16 (Phi=180.0_2_12.55) has 208 elements Group17 (Phi=180.0_2_22.80) has 368 elements and it goes up to group 82. My system is a protein and would like to analyse the dihedral angles. Is it possible for a protein systems? or this is only for the peptides? which group should I pick up? Best regards Urszula - Ta wiadomość została wysłana z serwera Uniwersytetu Gdańskiego http://www.ug.edu.pl/ -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] ramachandran plot
resolution. Change when changing the resolution. ) # Close the image file, saving it. dev.off() #---End of image--- On Mon, Nov 17, 2014 at 1:44 PM, Urszula Uciechowska urszula.uciechow...@biotech.ug.edu.pl wrote: Dear Tsjerk, Could you send me the script again? as I did not find the attachment in your previous email. best regards Urszula Hi Urszula, Attached is an R script for drawing 2D circular or combined circular/linear KDEs. It works as a command line script, taking as arguments a file with 2-column data, and an output image file name (./kde2d.r input.dat output.png). It's pretty easy to adapt to suit your needs, even if you don't know R specifically. I wrote the routine for a manuscript we just submitted, where the method is explained in some detail, and if you like the images and care to use it for publications, I would be obliged if you could reference that paper (High-Throughput Simulations of Dimer and Trimer Assembly of Membrane Proteins. The DAFT approach.). If you run into problems or have further questions, please let me know. Cheers, Tsjerk On Fri, Nov 14, 2014 at 4:31 PM, Urszula Uciechowska urszula.uciechow...@biotech.ug.edu.pl wrote: Could you please send me the code? It can be on my private email. Thanks a lot Ursuzla Hi Urszula, It's a while ago that I made that one, and I don't have the code at hand. But it's a combination of a density plot (kde2d) with the points laid over, and a polygon to highlight the forbidden region. These days I'm doing circular 2D KDEs, whic is more correct. I can send the R code for thay if you want. Best, Tsjerk On Nov 14, 2014 12:34 PM, Urszula Uciechowska urszula.uciechow...@biotech.ug.edu.pl wrote: Dear Gromacs users, I generated the ramachandran plot and would like to colour it in xmgrace as it was shown in tutorial: http://nmr.chem.uu.nl/~adrien/course/molmod/analysis2.html Does anyone know how to do it? Best regards Urszula Uciechowska - Ta wiadomość została wysłana z serwera Uniwersytetu Gdańskiego http://www.ug.edu.pl/ -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. University of Gdansk and Medical Univesity of Gdansk Department of Molecular and Cellular Biology ul. Kladki 24 80-822 Gdansk Poland - Ta wiadomość została wysłana z serwera Uniwersytetu Gdańskiego http://www.ug.edu.pl/ -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Tsjerk A. Wassenaar, Ph.D. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. University of Gdansk and Medical Univesity of Gdansk Department of Molecular and Cellular Biology ul. Kladki 24 80-822 Gdansk Poland - Ta wiadomość została wysłana z serwera Uniwersytetu Gdańskiego http://www.ug.edu.pl/ -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Tsjerk A. Wassenaar, Ph.D. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] ramachandran plot
Dear Tsjerk, Could you send me the script again? as I did not find the attachment in your previous email. best regards Urszula Hi Urszula, Attached is an R script for drawing 2D circular or combined circular/linear KDEs. It works as a command line script, taking as arguments a file with 2-column data, and an output image file name (./kde2d.r input.dat output.png). It's pretty easy to adapt to suit your needs, even if you don't know R specifically. I wrote the routine for a manuscript we just submitted, where the method is explained in some detail, and if you like the images and care to use it for publications, I would be obliged if you could reference that paper (High-Throughput Simulations of Dimer and Trimer Assembly of Membrane Proteins. The DAFT approach.). If you run into problems or have further questions, please let me know. Cheers, Tsjerk On Fri, Nov 14, 2014 at 4:31 PM, Urszula Uciechowska urszula.uciechow...@biotech.ug.edu.pl wrote: Could you please send me the code? It can be on my private email. Thanks a lot Ursuzla Hi Urszula, It's a while ago that I made that one, and I don't have the code at hand. But it's a combination of a density plot (kde2d) with the points laid over, and a polygon to highlight the forbidden region. These days I'm doing circular 2D KDEs, whic is more correct. I can send the R code for thay if you want. Best, Tsjerk On Nov 14, 2014 12:34 PM, Urszula Uciechowska urszula.uciechow...@biotech.ug.edu.pl wrote: Dear Gromacs users, I generated the ramachandran plot and would like to colour it in xmgrace as it was shown in tutorial: http://nmr.chem.uu.nl/~adrien/course/molmod/analysis2.html Does anyone know how to do it? Best regards Urszula Uciechowska - Ta wiadomość została wysłana z serwera Uniwersytetu Gdańskiego http://www.ug.edu.pl/ -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. University of Gdansk and Medical Univesity of Gdansk Department of Molecular and Cellular Biology ul. Kladki 24 80-822 Gdansk Poland - Ta wiadomość została wysłana z serwera Uniwersytetu Gdańskiego http://www.ug.edu.pl/ -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Tsjerk A. Wassenaar, Ph.D. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. University of Gdansk and Medical Univesity of Gdansk Department of Molecular and Cellular Biology ul. Kladki 24 80-822 Gdansk Poland - Ta wiadomość została wysłana z serwera Uniwersytetu Gdańskiego http://www.ug.edu.pl/ -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] ramachandran plot
Dear Gromacs users, I generated the ramachandran plot and would like to colour it in xmgrace as it was shown in tutorial: http://nmr.chem.uu.nl/~adrien/course/molmod/analysis2.html Does anyone know how to do it? Best regards Urszula Uciechowska - Ta wiadomość została wysłana z serwera Uniwersytetu Gdańskiego http://www.ug.edu.pl/ -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] hbond analysis
Dear Gromacs users, Regarding the g_hbond analysis. What does exactly represent the second and third column in hbond.xvg file (pasted below)? g_hbond is part of G R O M A C S: # # Gromacs Runs One Microsecond At Cannonball Speeds # @title Hydrogen Bonds @xaxis label Time @yaxis label Number @TYPE xy @ view 0.15, 0.15, 0.75, 0.85 @ legend on @ legend box on @ legend loctype view @ legend 0.78, 0.8 @ legend length 2 @ s0 legend Hydrogen bonds @ s1 legend Pairs within 0.35 nm 0 0 0 1 0 0 2 0 0 3 0 0 4 0 0 5 0 0 6 0 0 7 0 0 8 0 0 9 0 0 10 0 0 11 0 0 12 0 0 13 0 0 14 0 0 15 0 0 16 0 0 : Best regrads Urszula University of Gdansk and Medical Univesity of Gdansk Department of Molecular and Cellular Biology ul. Kladki 24 80-822 Gdansk Poland - Ta wiadomość została wysłana z serwera Uniwersytetu Gdańskiego http://www.ug.edu.pl/ -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] MD for DNA structure
Dear Gromacs users, I am trying to run MD for my DNA structure, however after typing grompp -f nvt.mdp -c em.gor -p top -o *.tpr I am getting an error message: Back Off! I just backed up mdout.mdp to ./#mdout.mdp.7# NOTE 1 [file nvt.mdp]: The Berendsen thermostat does not generate the correct kinetic energy distribution. You might want to consider using the V-rescale thermostat. Generated 2211 of the 2211 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 2211 of the 2211 1-4 parameter combinations Excluding 3 bonded neighbours molecule type 'DNA' turning all bonds into constraints... Excluding 2 bonded neighbours molecule type 'SOL' turning all bonds into constraints... Excluding 1 bonded neighbours molecule type 'NA' turning all bonds into constraints... Excluding 1 bonded neighbours molecule type 'CL' turning all bonds into constraints... Setting gen_seed to 17417 Velocities were taken from a Maxwell distribution at 310 K Analysing residue names: There are:46DNA residues There are: 39061 Water residues There are: 190Ion residues Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... --- Program grompp, VERSION 4.5.3 Source code file: readir.c, line: 1316 Fatal error: Group Non-Protein not found in indexfile. Maybe you have non-default goups in your mdp file, while not using the '-n' option of grompp. In that case use the '-n' option. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- My nvt.mdp file contains: 7.3.2 Preprocessing define = -DPOSRES ; defines to pass to the preprocessor ; 7.3.3 Run Control integrator = md; md integrator tinit = 0 ; [ps] starting time for run dt = 0.002 ; [ps] time step for integration nsteps = 10 ; maximum number of steps to integrate, 0.002 * 25,000 = 50 ps comm_mode = Linear; remove center of mass translation nstcomm = 1 ; [steps] frequency of mass motion removal comm_grps = Non-Protein ; group(s) for center of mass motion removal ; 7.3.8 Output Control nstxout = 25000 ; [steps] freq to write coordinates to trajectory nstvout = 25000 ; [steps] freq to write velocities to trajectory nstfout = 25000 ; [steps] freq to write forces to trajectory nstlog = 100 ; [steps] freq to write energies to log file nstenergy = 100 ; [steps] freq to write energies to energy file nstxtcout = 100 ; [steps] freq to write coordinates to xtc trajectory xtc_precision = 1000 ; [real] precision to write xtc trajectory xtc_grps= System; group(s) to write to xtc trajectory energygrps = System; group(s) to write to energy file ; 7.3.9 Neighbor Searching nstlist = 1 ; [steps] freq to update neighbor list ns_type = grid ; method of updating neighbor list pbc = xyz ; periodic boundary conditions in all directions rlist = 0.8 ; [nm] cut-off distance for the short-range neighbor list ; 7.3.10 Electrostatics coulombtype = PME ; Particle-Mesh Ewald electrostatics rcoulomb= 0.8 ; [nm] distance for Coulomb cut-off ; 7.3.11 VdW vdwtype = cut-off ; twin-range cut-off with rlist where rvdw = rlist rvdw= 0.8 ; [nm] distance for LJ cut-off DispCorr= EnerPres ; apply long range dispersion corrections ; 7.3.13 Ewald fourierspacing = 0.12 ; [nm] grid spacing for FFT grid when using PME pme_order = 4 ; interpolation order for PME, 4 = cubic ewald_rtol = 1e-5 ; relative strength of Ewald-shifted potential at rcoulomb ; 7.3.14 Temperature Coupling tcoupl = berendsen ; temperature coupling with Berendsen-thermostat tc_grps = Non-Protein ; groups to couple seperately to temperature bath tau_t = 0.1 ; [ps] time constant for coupling ref_t = 310 ; [K] reference temperature for coupling ; 7.3.17 Velocity Generation gen_vel = yes ; generate velocities according to Maxwell distribution of temperature
[gmx-users] hbond analysis
Dear gromacs users, I am having some problems with hbond analysis using gromacs. I am interested in hbonds between certain amino acids for example: LYS256 and nucleic acid that has number 2 in my files. I generated the index file which contains r256 and r2 by running make_ndx -f gro -o out.ndx then I run g_hbond g_hbond -f traj.xtc -s .tpr -num hydrogen-bonds-protein.xvg My xvg file did not contain any hbond between those amino acids, which is not true. I do not know what went wrong. Could anyone suggest me something? Is there any other way to run the hbond? Is it possible to use the xtc trajectory and run hbond anlysis in ptraj? or can I convert it somehow? Best regards Urszula Uciechowska University of Gdansk and Medical Univesity of Gdansk Department of Molecular and Cellular Biology ul. Kladki 24 80-822 Gdansk Poland - Ta wiadomość została wysłana z serwera Uniwersytetu Gdańskiego http://www.ug.edu.pl/ -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] question about walls for a simple water box
Dear Gromacs users, I am following the tutorial: http://www3.nd.edu/~gezelter/Teaching/650/exercises/gromacs/ and I want to use the command: g_rama -f ../full.trr -s ../full.tpr -o rama.xvg - I was wondering how to get the full.tpr file? is there any command to cat those files? I run MD for 50ns and I was extending my simulations every 10ns. Any suggestions? best regards Urszula Uciechowska --- University of Gdansk and Medical Univesity of Gdansk Department of Molecular and Cellular Biology ul. Kladki 24 80-822 Gdansk Poland - Ta wiadomość została wysłana z serwera Uniwersytetu Gdańskiego http://www.ug.edu.pl/ -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] combine tpr files?
Dear Gromacs users, I am following the tutorial: http://www3.nd.edu/~gezelter/Teaching/650/exercises/gromacs/ and I want to use the command: g_rama -f ../full.trr -s ../full.tpr -o rama.xvg - I was wondering how to get the full.tpr file? is there any command to cat those files? I run MD for 50ns and I was extending my simulations every 10ns. Any suggestions? best regards Urszula Uciechowska - Ta wiadomość została wysłana z serwera Uniwersytetu Gdańskiego http://www.ug.edu.pl/ -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] binding Free energy
Dear gromacs user, I would like to calculate Binding Free Energy Calculations for my protein-DNA complex (already run for 50ns). Is there any manual or tutorial (for more complex systems) available? best regards Urszula - Ta wiadomość została wysłana z serwera Uniwersytetu Gdańskiego http://www.ug.edu.pl/ -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] gromacs error
How should I correct the input file? Urszula Uciechowska On 7/31/14, 7:42 AM, Urszula Uciechowska wrote: Dear Gromacs users, I tried to run coarse grained MD however after a few steps I got: Step 39, time 0.78 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.038933, max 2.260527 (between atoms 10459 and 10463) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 10457 10459 89.80.3107 0.8288 0.3100 10459 10463 90.30.3075 1.0108 0.3100 10463 10467 90.60.3084 0.8774 0.3100 10467 10469 81.10.3103 0.3823 0.3100 10469 10471 90.30.3121 0.1885 0.3100 Wrote pdb files with previous and current coordinates Step 40, time 0.8 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 165002.767686, max 10334958.00 (between atoms 10457 and 10459) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 10443 10445 30.10.3100 0.3581 0.3100 10445 10447 102.20.3102 266.6146 0.3100 10447 10450 59.30.3100 624.1382 0.3100 10450 10452 101.40.3105 5390.4609 0.3100 10452 10454 87.90.3083 104154.3047 0.3100 10454 10457 83.90.3497 439143.5312 0.3100 10457 10459 87.50.8288 3203837.2500 0.3100 10459 10463 87.81.0108 2960821.2500 0.3100 10463 10467 95.20.8774 763857.8125 0.3100 10467 10469 95.50.3823 195859.2656 0.3100 10469 10471 104.30.1885 43565.4141 0.3100 10471 10473 90.30.3534 7857.3394 0.3100 10473 10475 105.50.3125 57.7529 0.3100 10475 10477 90.00.3099 0.3849 0.3100 10477 10480 32.40.3101 0.3647 0.3100 Wrote pdb files with previous and current coordinates mpiexec: process_obit_event: evt 6 task 0 on wn518 stat 267. mpiexec: wait_tasks: waiting for wn350 wn350 wn501. mpiexec: kill_others_now: alarm went off, killing all other tasks. mpiexec: kill_tasks: killing all tasks. mpiexec: process_kill_event: evt 10 task 1 on wn350. mpiexec: process_kill_event: evt 12 task 3 on wn501. mpiexec: process_kill_event: evt 11 task 2 on wn350. mpiexec: process_obit_event: evt 7 task 3 on wn501 stat 265. mpiexec: process_obit_event: evt 8 task 1 on wn350 stat 265. mpiexec: process_obit_event: evt 9 task 2 on wn350 stat 265. mpiexec: Warning: task 0 died with signal 11 (Segmentation fault). mpiexec: Warning: tasks 1-3 died with signal 9 (Killed). in log file last line is: Constraining the starting coordinates (step 0) Constraining the coordinates at t0-dt (step 0) RMS relative constraint deviation after constraining: 4.04e-06 Initial temperature: 1.8161e-07 K Started mdrun on node 0 Wed Jul 30 10:39:50 2014 Step Time Lambda 00.00.0 Grid: 42 x 42 x 42 cells Energies (kJ/mol) Bond G96AngleProper Dih. Improper Dih.LJ (SR) 6.24872e+031.47844e+041.75778e+034.11810e+02 -2.32179e+07 Coulomb (SR) Position Rest. PotentialKinetic En. Total Energy -4.49776e+032.00073e-01 -2.31992e+071.44043e+01 -2.31992e+07 Temperature Pressure (bar) Constr. rmsd 1.55259e-03 -1.41563e+035.56533e-06 my input file: define = -DPOSRES dt = 0.02 nsteps = 25000 nstxout = 0 nstvout = 0 nstlog = 100 nstxtcout= 100 xtc-precision= 10 rlist= 1.4 coulombtype = shift rcoulomb = 1.2 epsilon_r= 15 vdw-type = shift rvdw-switch = 0.9 rvdw = 1.2 tcoupl = v-rescale tc-grps = Protein W tau-t= 1.0 1.0 ref-t= 300 300 Pcoupl = Berendsen Pcoupltype = isotropic tau-p= 12.0 compressibility = 3e-4 ref-p= 1.0 refcoord_scaling = com What is wrong here? Likely this: Initial temperature: 1.8161e-07 K You haven't generated any velocities, so your system is effectively frozen, and you're simultaneously applying a thermostat and barostat, which probably cause your velocities to go absolutely insane, blowing up the system. Generate velocities at the desired temperature and equilibrate gently. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs
Re: [gmx-users] gromacs error
; LINear Constraint Solver continuation= yes ; apply constraints to the start configuration lincs_order = 4 ; highest order in the expansion of the contraint coupling matrix lincs_iter = 1 ; number of iterations to correct for rotational lengthening lincs_warnangle = 30; [degrees] maximum angle that a bond can rotate before LINCS will complain (END) Best regards Urszula Uciechowska - Ta wiadomość została wysłana z serwera Uniwersytetu Gdańskiego http://www.ug.edu.pl/ -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] input error?
I have changed the Pcoupl into parrinello-rahman and I have still the same error. The input file was taken from the martini webpage http://md.chem.rug.nl/cgmartini/index.php/proteins define = -DPOSRES dt = 0.02 nsteps = 25000 nstxout = 0 nstvout = 0 nstlog = 100 nstxtcout= 100 xtc-precision= 10 rlist= 1.4 coulombtype = shift rcoulomb = 1.2 epsilon_r= 15 vdw-type = shift rvdw-switch = 0.9 rvdw = 1.2 tcoupl = v-rescale tc-grps = Protein W tau-t= 1.0 1.0 ref-t= 300 300 Pcoupl = parrinello-rahman Pcoupltype = isotropic tau-p= 12.0 compressibility = 3e-4 ref-p= 1.0 refcoord_scaling = all Urszula Uciechowska ~ - Ta wiadomość została wysłana z serwera Uniwersytetu Gdańskiego http://www.ug.edu.pl/ -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] min in vacuum
Hi gromacs users, I am trying to run coarse-grained MD for a protein system using martini protocol. First step is to run short min in vacuum, whenever I try to do this I am getting an error regarding my input file. ERROR 1 [file system-vaccum.top, line 16]: ERROR: The cut-off length is longer than half the shortest box vector or longer than the smallest box diagonal element. Increase the box size or decrease rlist. There was 1 note --- Program grompp, VERSION 4.5.3 Source code file: grompp.c, line: 1356 Fatal error: There was 1 error in input file(s) For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- I Caught It In the Face (P.J. Harvey) My input file: integrator = steep dt = 0.02 nsteps = 10 nstxout = 0 nstvout = 0 nstlog = 100 nstxtcout= 100 xtc-precision= 10 rlist= 1.4 coulombtype = shift rcoulomb = 1.2 epsilon_r= 15 vdw-type = shift rvdw-switch = 0.9 rvdw = 1.2 tcoupl = v-rescale tc-grps = Protein tau-t= 1.0 ref-t= 300 How should I modify it? Thank you in advance for any suggestions. best regards Urszula - Ta wiadomość została wysłana z serwera Uniwersytetu Gdańskiego http://www.ug.edu.pl/ -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] rlist for implicit water
Dear Justin, How could I change the cut-offs to make the MD more faster in my case? /Urszula On 6/3/14, 4:15 AM, Urszula Uciechowska wrote: Dear Gromacs users, I would like to run simulations with implicit water. My protein system is quite big it contains 784AA. I prepared eM.mdp file (see below) however I am not sure if its ok especially the rlist what should I use there in case of such big system. define = -DFLEXIBLE constraints = none integrator = steep ; steepest descents energy minimization dt = 0.001 ; ps nsteps = 3000 ; maximum number of steps to integrate implicit_solvent= GBSA gb_algorithm= Still nstgbradii = 1 gb_epsilon_solvent = 80 gb_saltconc = 0 sa_algorithm= Ace-approximation sa_surface_tension = -1 pbc = no rgbradii= 0 ns_type = simple; method of updating neighbor list nstlist = 0 rlist = 0 ; this means all-vs-all (no cut-off) coulombtype = cut-off rcoulomb= 0 ; [nm] distance for Coulomb cut-off vdwtype = cut-off ; twin-range cut-off with rlist where rvdw = rlist rvdw= 0 ; [nm] distance for LJ cut-off nstenergy = 100 emtol = 5.0 emstep = 0.01 comm-grps = Protein optimize_fft= yes Thank you in advance for any comments and suggestions. If you're using infinite cutoffs, the only acceptable value for rlist is 0. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. - Ta wiadomość została wysłana z serwera Uniwersytetu Gdańskiego http://www.ug.edu.pl/ -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] need you help - New user
Dear Gromacs users, I am having problem running NVT calculation, when is finished I do not see the *.gro file among the out file. I do not know what the problem can be. I am not getting any error. The command that I used: mdrun -s input_nvt.tpr -deffnm nvt -v in .Log file I have R E A L C Y C L E A N D T I M E A C C O U N T I N G Computing: Nodes Number G-CyclesSeconds % --- Domain decomp. 6770 1779.164 785.2 5.5 DD comm. load 6769 10.5824.7 0.0 DD comm. bounds6769 11.2465.0 0.0 Send X to PME 6770 37.780 16.7 0.1 Comm. coord. 6770 71.593 31.6 0.2 Neighbor search6770 5301.193 2339.716.5 Force 6770 5327.504 2351.316.6 Wait + Comm. F 6770 1984.758 876.0 6.2 PME mesh 6770 5970.668 2635.118.6 Wait + Comm. X/F 6 10102.647 4458.831.4 Wait + Recv. PME F 6770 36.705 16.2 0.1 Write traj.6 10 21.6449.6 0.1 Update 6770 205.313 90.6 0.6 Constraints6770 778.976 343.8 2.4 Comm. energies 6771 301.011 132.9 0.9 Rest 6 208.397 92.0 0.6 --- Total 12 32149.18014189.0 100.0 --- --- PME redist. X/F6 1540 565.866 249.7 1.8 PME spread/gather 6 1540 2972.849 1312.1 9.2 PME 3D-FFT 6 1540 1841.695 812.8 5.7 PME solve 6770 590.096 260.4 1.8 --- Parallel run - timing based on wallclock. NODE (s) Real (s) (%) Time: 1182.415 1182.415100.0 19:42 (Mnbf/s) (GFlops) (ns/day) (hour/ns) Performance:129.307 11.117 0.113213.278 Finished mdrun on node 0 Mon Jun 2 11:00:09 2014 (END) Thank you for your help. Urszula Uciechowska - Ta wiadomość została wysłana z serwera Uniwersytetu Gdańskiego http://www.ug.edu.pl/ -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] need you help - New user
It is still not there. I have also tried to use command: $MDRUN -v -s nvt.tpr -o nvt.trr -x nvt.xtc -c nvt.gro -g nvt.log -e nvt nvt.edr I am using gromacs/4.5.3-s. Before sumbitting NVT I run simple energy min. I attached my NVT.mdp file... I do not know what is wrong.. Please suggest me something /Urszula Try using the following command mdrun -v -deffnm nvt On Mon, Jun 2, 2014 at 11:23 AM, Urszula Uciechowska urszula.uciechow...@biotech.ug.edu.pl wrote: Dear Gromacs users, I am having problem running NVT calculation, when is finished I do not see the *.gro file among the out file. I do not know what the problem can be. I am not getting any error. The command that I used: mdrun -s input_nvt.tpr -deffnm nvt -v in .Log file I have R E A L C Y C L E A N D T I M E A C C O U N T I N G Computing: Nodes Number G-CyclesSeconds % --- Domain decomp. 6770 1779.164 785.2 5.5 DD comm. load 6769 10.5824.7 0.0 DD comm. bounds6769 11.2465.0 0.0 Send X to PME 6770 37.780 16.7 0.1 Comm. coord. 6770 71.593 31.6 0.2 Neighbor search6770 5301.193 2339.716.5 Force 6770 5327.504 2351.316.6 Wait + Comm. F 6770 1984.758 876.0 6.2 PME mesh 6770 5970.668 2635.118.6 Wait + Comm. X/F 6 10102.647 4458.831.4 Wait + Recv. PME F 6770 36.705 16.2 0.1 Write traj.6 10 21.6449.6 0.1 Update 6770 205.313 90.6 0.6 Constraints6770 778.976 343.8 2.4 Comm. energies 6771 301.011 132.9 0.9 Rest 6 208.397 92.0 0.6 --- Total 12 32149.18014189.0 100.0 --- --- PME redist. X/F6 1540 565.866 249.7 1.8 PME spread/gather 6 1540 2972.849 1312.1 9.2 PME 3D-FFT 6 1540 1841.695 812.8 5.7 PME solve 6770 590.096 260.4 1.8 --- Parallel run - timing based on wallclock. NODE (s) Real (s) (%) Time: 1182.415 1182.415100.0 19:42 (Mnbf/s) (GFlops) (ns/day) (hour/ns) Performance:129.307 11.117 0.113213.278 Finished mdrun on node 0 Mon Jun 2 11:00:09 2014 (END) Thank you for your help. Urszula Uciechowska - Ta wiadomość została wysłana z serwera Uniwersytetu Gdańskiego http://www.ug.edu.pl/ -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. - Ta wiadomość została wysłana z serwera Uniwersytetu Gdańskiego http://www.ug.edu.pl/-- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] grompp
Dear Gromacs users, I am new to Gromacs. I am trying to add ions to my protein system. After typing command: grompp -f grompp.mdp -c EcoLon6mer-sol.gro -p EcoLon6mer.top -o genion_input.tpr where the grompp.mdp contains: ; ions.mdp - used as input into grompp to generate ions.tpr ; Parameters describing what to do, when to stop and what to save integrator = steep ; Algorithm (steep = steepest descent minimization) emtol = 1000.0; Stop minimization when the maximum force 1000.0 kJ/mol/nm emstep = 0.01 ; Energy step size nsteps = 5 ; Maximum number of (minimization) steps to perform ; Parameters describing how to find the neighbors of each atom and how to calculate the interactions nstlist = 1 ; Frequency to update the neighbor list and long range forces ns_type = grid ; Method to determine neighbor list (simple, grid) rlist = 1.0 ; Cut-off for making neighbor list (short range forces) coulombtype = PME ; Treatment of long range electrostatic interactions rcoulomb= 1.0 ; Short-range electrostatic cut-off rvdw= 1.0 ; Short-range Van der Waals cut-off pbc = xyz ; Periodic Boundary Conditions (yes/no) I am getting an error message: Back Off! I just backed up mdout.mdp to ./#mdout.mdp.5# checking input for internal consistency... processing topology... Opening library file /software/local/Gromacs/4.5.3/Intel-ompi-fftw/share/gromacs/top/amber99.ff/forcefield.itp --- Program grompp, VERSION 4.0.7 Source code file: futil.c, line: 526 Fatal error: Library file ffnonbonded.itp not found in current dir nor in your GMXLIB path. --- Disturb the Peace of a John Q Citizen (Urban Dance Squad) How can I solve this problem? How can I add the path? best regards Urszula - Ta wiadomość została wysłana z serwera Uniwersytetu Gdańskiego http://www.ug.edu.pl/ -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
