[gmx-users] g_lie query
Hi ALL, I have run a protein + ligand (dopamine) simulation. Now I want to calculate the free energy of binding using g_lie. But g_lie asks for two values: Elj and Eqq. How or from where can I get these values for my ligand? Also, do I need to run a simulation with only the ligand? And, is there any other way (like MMGBSA in Amber) to calculate the free energy for my simulation? Any suggestion is welcome. Thanks a lot in advance. Regards, Anirban -- 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] no-pbc simulation in parallel
Hi all, I am experiencing a strange error while trying to perform a parallel run with pbc=no. Just a core.*** file (at the very beginning) is created and nothing is written into the logfile. The simulation just stops. I use mpirun -np 8 mdrun_407f -pd 2 2 2 . The same system runs correctly if PBC=XYZ. The system is rather big - 10x10x10nm with ~40 000 atoms My parameters are below: == integrator = md dt = 0.0025 nstxout = 0 nstvout = 0 nstfout = 0 emtol= 100 nsteps = 5 nstlog = 5000 nstenergy= 1000 nstxtcout= 1000 xtc-precision= 1000 nstlist = 5 comm_mode = ANGULAR ns_type = simple pbc = no rlist= 1.4 coulombtype = cut-off rcoulomb = 1.4 vdw-type = shift rvdw-switch = 1.2 rvdw = 1.3 DispCorr = no table-extension = 1 Tcoupl = V-rescale tc-grps = System tau_t= 0.1 ref_t= 373 ;Pcoupl = no ;Parrinello-Rahman ;Pcoupltype = isotropic ;tau_p= 0.5 ;compressibility = 4.5e-5 ;ref_p= 100 == Is it a bug or what? Thank you. Dr. Vitaly Chaban -- 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] Charge grps and cut-off
Hi, This is the .mdp file that produces notes-3 and 4. However, the previous md file produces note-3. ; RUN CONTROL PARAMETERS integrator = md dt = 0.002 nsteps = 500 ; OUTPUT CONTROL OPTIONS nstxout = 0; No output, except for last frame (coordinates) nstvout = 0; No output, except for last frame (velocities) nstfout = 0; No output, except for last frame (forces) nstlog = 50; Write every step to the log nstenergy= 50; Write energies at every step xtc_grps = Protein nstxtcout= 50; Do not write a compressed trajectory energygrps = Protein Non-Protein ; Write energy information separately for these groups ; NEIGHBORSEARCHING PARAMETERS nstlist = 5 ns-type = Grid pbc = xyz rlist= 2.0 ; OPTIONS FOR ELECTROSTATICS AND VDW coulombtype = Reaction-field-zero rcoulomb = 1.8 epsilon_rf = 0 vdw-type = Switch rvdw = 2.0 rvdw-switch = 1.6 ; Spacing for the PME/PPPM FFT fourierspacing = 0.12 ; 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= 4 ewald_rtol = 1e-05 epsilon_surface = 0 optimize_fft = no ; Temperature coupling tcoupl = nose-hoover tc-grps = Protein Non-Protein tau_t= 0.2 0.2 ref_t= 300 300 ; Pressure coupling pcoupl = no ; OPTIONS FOR BONDS constraints = all-bonds constraint-algorithm = SHAKE shake_tol= 0.0001 Pooja On Fri, Jul 16, 2010 at 8:51 PM, Justin A. Lemkul jalem...@vt.edu wrote: Sai Pooja wrote: Hi, I am trying to reproduce results from a paper which uses this cutoff. The work is on loop-folding and they use implicit solvent. I am using explicit solvent with charmm 27. Below is my mdp file. I am not sure if there is any advantage in using a large cut-off. Large cutoffs can cause artifacts. This .mdp file also does not match the error message you quoted before. If it is indeed accurate, then it looks like your .mdp file is being interpreted incorrectly (2.0-nm cutoffs instead of 1.8 nm). If there is a misinterpretation, file a bugzilla. If you've simply posted the wrong file, please post the correct file, if necessary. But I'd suggest you do some homework about the effects of long cutoffs, especially if they deviate from what the force field derivation requires. -Justin ; VARIOUS PREPROCESSING OPTIONS title= NVT simulation (constant number, pressure and temperature) cpp = /lib/cpp define =-DPOSRES ; RUN CONTROL PARAMETERS integrator = md dt = 0.002 nsteps = 10 ; OUTPUT CONTROL OPTIONS nstxout = 1 nstvout = 0 nstfout = 0 nstlog = 1 nstenergy= 1 nstxtcout= 0 xtc_precision= 0 xtc-grps = System energygrps = Protein Non-Protein ; NEIGHBORSEARCHING PARAMETERS nstlist = 5 ns-type = Grid pbc = xyz rlist= 1.8 ; OPTIONS FOR ELECTROSTATICS AND VDW coulombtype = PME fourierspacing = 0.12 rcoulomb = 1.8 epsilon_rf = 78 vdw-type = Cut-off rvdw = 1.8 ; 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= 4 ewald_rtol = 1e-05 epsilon_surface = 0 optimize_fft = no ; Temperature coupling Tcoupl = Berendsen tc-grps = Protein Non-Protein tau_t= 0.2 0.2 ref_t= 300 300 ; Pressure coupling Pcoupl = Berendsen Pcoupltype = Isotropic tau_p= 1.0 compressibility = 4.5e-5 ref_p= 1.0 ; GENERATE VELOCITIES FOR STARTUP RUN gen_vel = no; Assign velocities to particles by taking them randomly from a Maxwell distribution gen_temp = 300.0 ; Temperature to generate corresponding Maxwell distribution
Re: [gmx-users] Charge grps and cut-off
Sai Pooja wrote: Hi, This is the .mdp file that produces notes-3 and 4. However, the previous md file produces note-3. ; RUN CONTROL PARAMETERS integrator = md dt = 0.002 nsteps = 500 ; OUTPUT CONTROL OPTIONS nstxout = 0; No output, except for last frame (coordinates) nstvout = 0; No output, except for last frame (velocities) nstfout = 0; No output, except for last frame (forces) nstlog = 50; Write every step to the log nstenergy= 50; Write energies at every step xtc_grps = Protein nstxtcout= 50; Do not write a compressed trajectory energygrps = Protein Non-Protein ; Write energy information separately for these groups ; NEIGHBORSEARCHING PARAMETERS nstlist = 5 ns-type = Grid pbc = xyz rlist= 2.0 ; OPTIONS FOR ELECTROSTATICS AND VDW coulombtype = Reaction-field-zero rcoulomb = 1.8 epsilon_rf = 0 vdw-type = Switch rvdw = 2.0 rvdw-switch = 1.6 Well, here's the problem. Read about proper usage of the switch function, especially the note about the size of rlist: http://manual.gromacs.org/current/online/mdp_opt.html#vdw -Justin ; Spacing for the PME/PPPM FFT fourierspacing = 0.12 ; 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= 4 ewald_rtol = 1e-05 epsilon_surface = 0 optimize_fft = no ; Temperature coupling tcoupl = nose-hoover tc-grps = Protein Non-Protein tau_t= 0.2 0.2 ref_t= 300 300 ; Pressure coupling pcoupl = no ; OPTIONS FOR BONDS constraints = all-bonds constraint-algorithm = SHAKE shake_tol= 0.0001 Pooja On Fri, Jul 16, 2010 at 8:51 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: Sai Pooja wrote: Hi, I am trying to reproduce results from a paper which uses this cutoff. The work is on loop-folding and they use implicit solvent. I am using explicit solvent with charmm 27. Below is my mdp file. I am not sure if there is any advantage in using a large cut-off. Large cutoffs can cause artifacts. This .mdp file also does not match the error message you quoted before. If it is indeed accurate, then it looks like your .mdp file is being interpreted incorrectly (2.0-nm cutoffs instead of 1.8 nm). If there is a misinterpretation, file a bugzilla. If you've simply posted the wrong file, please post the correct file, if necessary. But I'd suggest you do some homework about the effects of long cutoffs, especially if they deviate from what the force field derivation requires. -Justin ; VARIOUS PREPROCESSING OPTIONS title= NVT simulation (constant number, pressure and temperature) cpp = /lib/cpp define =-DPOSRES ; RUN CONTROL PARAMETERS integrator = md dt = 0.002 nsteps = 10 ; OUTPUT CONTROL OPTIONS nstxout = 1 nstvout = 0 nstfout = 0 nstlog = 1 nstenergy= 1 nstxtcout= 0 xtc_precision= 0 xtc-grps = System energygrps = Protein Non-Protein ; NEIGHBORSEARCHING PARAMETERS nstlist = 5 ns-type = Grid pbc = xyz rlist= 1.8 ; OPTIONS FOR ELECTROSTATICS AND VDW coulombtype = PME fourierspacing = 0.12 rcoulomb = 1.8 epsilon_rf = 78 vdw-type = Cut-off rvdw = 1.8 ; 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= 4 ewald_rtol = 1e-05 epsilon_surface = 0 optimize_fft = no ; Temperature coupling Tcoupl
Re: [gmx-users] g_lie query
Anirban Ghosh wrote: Hi ALL, I have run a protein + ligand (dopamine) simulation. Now I want to calculate the free energy of binding using g_lie. But g_lie asks for two values: Elj and Eqq. How or from where can I get these values for my ligand? Also, do I need to run a simulation with only the ligand? And, is there any other way (like MMGBSA in Amber) to calculate the free energy for my simulation? Any suggestion is welcome. Thanks a lot in advance. Go to the literature and understand what information is needed for such a simulation, and then look into the list archives and you'll find dozens of threads about using g_lie. -Justin Regards, Anirban -- 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 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] Charge grps and cut-off
Thanks Justin. How about note 3? The largest charge group contains 12 atoms. Since atoms only see each other when the centers of geometry of the charge groups they belong to are within the cut-off distance, too large charge groups can lead to serious cut-off artifacts. For efficiency and accuracy, charge group should consist of a few atoms. For all-atom force fields use: CH3, CH2, CH, NH2, NH, OH, CO2, CO, etc. This note reappears no matter what the parameter file has. Does this mean I need to make changes in my top file or define charge groups? Pooja On Sat, Jul 17, 2010 at 7:25 AM, Justin A. Lemkul jalem...@vt.edu wrote: Sai Pooja wrote: Hi, This is the .mdp file that produces notes-3 and 4. However, the previous md file produces note-3. ; RUN CONTROL PARAMETERS integrator = md dt = 0.002 nsteps = 500 ; OUTPUT CONTROL OPTIONS nstxout = 0; No output, except for last frame (coordinates) nstvout = 0; No output, except for last frame (velocities) nstfout = 0; No output, except for last frame (forces) nstlog = 50; Write every step to the log nstenergy= 50; Write energies at every step xtc_grps = Protein nstxtcout= 50; Do not write a compressed trajectory energygrps = Protein Non-Protein ; Write energy information separately for these groups ; NEIGHBORSEARCHING PARAMETERS nstlist = 5 ns-type = Grid pbc = xyz rlist= 2.0 ; OPTIONS FOR ELECTROSTATICS AND VDW coulombtype = Reaction-field-zero rcoulomb = 1.8 epsilon_rf = 0 vdw-type = Switch rvdw = 2.0 rvdw-switch = 1.6 Well, here's the problem. Read about proper usage of the switch function, especially the note about the size of rlist: http://manual.gromacs.org/current/online/mdp_opt.html#vdw -Justin ; Spacing for the PME/PPPM FFT fourierspacing = 0.12 ; 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= 4 ewald_rtol = 1e-05 epsilon_surface = 0 optimize_fft = no ; Temperature coupling tcoupl = nose-hoover tc-grps = Protein Non-Protein tau_t= 0.2 0.2 ref_t= 300 300 ; Pressure coupling pcoupl = no ; OPTIONS FOR BONDS constraints = all-bonds constraint-algorithm = SHAKE shake_tol= 0.0001 Pooja On Fri, Jul 16, 2010 at 8:51 PM, Justin A. Lemkul jalem...@vt.edumailto: jalem...@vt.edu wrote: Sai Pooja wrote: Hi, I am trying to reproduce results from a paper which uses this cutoff. The work is on loop-folding and they use implicit solvent. I am using explicit solvent with charmm 27. Below is my mdp file. I am not sure if there is any advantage in using a large cut-off. Large cutoffs can cause artifacts. This .mdp file also does not match the error message you quoted before. If it is indeed accurate, then it looks like your .mdp file is being interpreted incorrectly (2.0-nm cutoffs instead of 1.8 nm). If there is a misinterpretation, file a bugzilla. If you've simply posted the wrong file, please post the correct file, if necessary. But I'd suggest you do some homework about the effects of long cutoffs, especially if they deviate from what the force field derivation requires. -Justin ; VARIOUS PREPROCESSING OPTIONS title= NVT simulation (constant number, pressure and temperature) cpp = /lib/cpp define =-DPOSRES ; RUN CONTROL PARAMETERS integrator = md dt = 0.002 nsteps = 10 ; OUTPUT CONTROL OPTIONS nstxout = 1 nstvout = 0 nstfout = 0 nstlog = 1 nstenergy= 1 nstxtcout= 0 xtc_precision= 0 xtc-grps = System energygrps = Protein Non-Protein ; NEIGHBORSEARCHING PARAMETERS nstlist = 5 ns-type = Grid pbc = xyz rlist= 1.8 ;
Re: [gmx-users] Charge grps and cut-off
Sai Pooja wrote: Thanks Justin. How about note 3? The largest charge group contains 12 atoms. Since atoms only see each other when the centers of geometry of the charge groups they belong to are within the cut-off distance, too large charge groups can lead to serious cut-off artifacts. For efficiency and accuracy, charge group should consist of a few atoms. For all-atom force fields use: CH3, CH2, CH, NH2, NH, OH, CO2, CO, etc. This note reappears no matter what the parameter file has. Does this mean I need to make changes in my top file or define charge groups? Yes, something is wrong with the topology. You have a charge group that is likely unacceptably large. -Justin Pooja On Sat, Jul 17, 2010 at 7:25 AM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: Sai Pooja wrote: Hi, This is the .mdp file that produces notes-3 and 4. However, the previous md file produces note-3. ; RUN CONTROL PARAMETERS integrator = md dt = 0.002 nsteps = 500 ; OUTPUT CONTROL OPTIONS nstxout = 0; No output, except for last frame (coordinates) nstvout = 0; No output, except for last frame (velocities) nstfout = 0; No output, except for last frame (forces) nstlog = 50; Write every step to the log nstenergy= 50; Write energies at every step xtc_grps = Protein nstxtcout= 50; Do not write a compressed trajectory energygrps = Protein Non-Protein ; Write energy information separately for these groups ; NEIGHBORSEARCHING PARAMETERS nstlist = 5 ns-type = Grid pbc = xyz rlist= 2.0 ; OPTIONS FOR ELECTROSTATICS AND VDW coulombtype = Reaction-field-zero rcoulomb = 1.8 epsilon_rf = 0 vdw-type = Switch rvdw = 2.0 rvdw-switch = 1.6 Well, here's the problem. Read about proper usage of the switch function, especially the note about the size of rlist: http://manual.gromacs.org/current/online/mdp_opt.html#vdw -Justin ; Spacing for the PME/PPPM FFT fourierspacing = 0.12 ; 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= 4 ewald_rtol = 1e-05 epsilon_surface = 0 optimize_fft = no ; Temperature coupling tcoupl = nose-hoover tc-grps = Protein Non-Protein tau_t= 0.2 0.2 ref_t= 300 300 ; Pressure coupling pcoupl = no ; OPTIONS FOR BONDS constraints = all-bonds constraint-algorithm = SHAKE shake_tol= 0.0001 Pooja On Fri, Jul 16, 2010 at 8:51 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu wrote: Sai Pooja wrote: Hi, I am trying to reproduce results from a paper which uses this cutoff. The work is on loop-folding and they use implicit solvent. I am using explicit solvent with charmm 27. Below is my mdp file. I am not sure if there is any advantage in using a large cut-off. Large cutoffs can cause artifacts. This .mdp file also does not match the error message you quoted before. If it is indeed accurate, then it looks like your .mdp file is being interpreted incorrectly (2.0-nm cutoffs instead of 1.8 nm). If there is a misinterpretation, file a bugzilla. If you've simply posted the wrong file, please post the correct file, if necessary. But I'd suggest you do some homework about the effects of long cutoffs, especially if they deviate from what the force field derivation requires. -Justin ; VARIOUS PREPROCESSING OPTIONS title= NVT simulation (constant number, pressure and temperature) cpp = /lib/cpp
Re: [gmx-users] Charge grps and cut-off
If gromacs assumes the aminoacid residues as charge groups by default then I have many residues which have 12 atoms since I am using an all-atom force field-charmm27(counting H). Is there a way to define charge groups? On Sat, Jul 17, 2010 at 7:41 AM, Justin A. Lemkul jalem...@vt.edu wrote: Sai Pooja wrote: Thanks Justin. How about note 3? The largest charge group contains 12 atoms. Since atoms only see each other when the centers of geometry of the charge groups they belong to are within the cut-off distance, too large charge groups can lead to serious cut-off artifacts. For efficiency and accuracy, charge group should consist of a few atoms. For all-atom force fields use: CH3, CH2, CH, NH2, NH, OH, CO2, CO, etc. This note reappears no matter what the parameter file has. Does this mean I need to make changes in my top file or define charge groups? Yes, something is wrong with the topology. You have a charge group that is likely unacceptably large. -Justin Pooja On Sat, Jul 17, 2010 at 7:25 AM, Justin A. Lemkul jalem...@vt.edumailto: jalem...@vt.edu wrote: Sai Pooja wrote: Hi, This is the .mdp file that produces notes-3 and 4. However, the previous md file produces note-3. ; RUN CONTROL PARAMETERS integrator = md dt = 0.002 nsteps = 500 ; OUTPUT CONTROL OPTIONS nstxout = 0; No output, except for last frame (coordinates) nstvout = 0; No output, except for last frame (velocities) nstfout = 0; No output, except for last frame (forces) nstlog = 50; Write every step to the log nstenergy= 50; Write energies at every step xtc_grps = Protein nstxtcout= 50; Do not write a compressed trajectory energygrps = Protein Non-Protein ; Write energy information separately for these groups ; NEIGHBORSEARCHING PARAMETERS nstlist = 5 ns-type = Grid pbc = xyz rlist= 2.0 ; OPTIONS FOR ELECTROSTATICS AND VDW coulombtype = Reaction-field-zero rcoulomb = 1.8 epsilon_rf = 0 vdw-type = Switch rvdw = 2.0 rvdw-switch = 1.6 Well, here's the problem. Read about proper usage of the switch function, especially the note about the size of rlist: http://manual.gromacs.org/current/online/mdp_opt.html#vdw -Justin ; Spacing for the PME/PPPM FFT fourierspacing = 0.12 ; 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= 4 ewald_rtol = 1e-05 epsilon_surface = 0 optimize_fft = no ; Temperature coupling tcoupl = nose-hoover tc-grps = Protein Non-Protein tau_t= 0.2 0.2 ref_t= 300 300 ; Pressure coupling pcoupl = no ; OPTIONS FOR BONDS constraints = all-bonds constraint-algorithm = SHAKE shake_tol= 0.0001 Pooja On Fri, Jul 16, 2010 at 8:51 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu wrote: Sai Pooja wrote: Hi, I am trying to reproduce results from a paper which uses this cutoff. The work is on loop-folding and they use implicit solvent. I am using explicit solvent with charmm 27. Below is my mdp file. I am not sure if there is any advantage in using a large cut-off. Large cutoffs can cause artifacts. This .mdp file also does not match the error message you quoted before. If it is indeed accurate, then it looks like your .mdp file is being interpreted incorrectly (2.0-nm cutoffs instead of 1.8 nm). If there is a misinterpretation, file a bugzilla. If you've simply posted the wrong file, please post the correct file, if necessary. But I'd suggest you do some homework about the effects of long cutoffs, especially if they deviate
Re: [gmx-users] Charge grps and cut-off
Sai Pooja wrote: If gromacs assumes the aminoacid residues as charge groups by default then I have many residues which have 12 atoms since I am using an all-atom force field-charmm27(counting H). It doesn't matter how many atoms are in a residue, it matters how many atoms are assigned to a single charge group and how large the resulting group will be. Is there a way to define charge groups? Charge groups are defined in the .rtp file, and you can see which one has 12 atoms in it by looking at your topology and watching the cgnr column. If pdb2gmx produced this large charge group, I'd suspect that's a problem that needs to be fixed. -Justin On Sat, Jul 17, 2010 at 7:41 AM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: Sai Pooja wrote: Thanks Justin. How about note 3? The largest charge group contains 12 atoms. Since atoms only see each other when the centers of geometry of the charge groups they belong to are within the cut-off distance, too large charge groups can lead to serious cut-off artifacts. For efficiency and accuracy, charge group should consist of a few atoms. For all-atom force fields use: CH3, CH2, CH, NH2, NH, OH, CO2, CO, etc. This note reappears no matter what the parameter file has. Does this mean I need to make changes in my top file or define charge groups? Yes, something is wrong with the topology. You have a charge group that is likely unacceptably large. -Justin Pooja On Sat, Jul 17, 2010 at 7:25 AM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu wrote: Sai Pooja wrote: Hi, This is the .mdp file that produces notes-3 and 4. However, the previous md file produces note-3. ; RUN CONTROL PARAMETERS integrator = md dt = 0.002 nsteps = 500 ; OUTPUT CONTROL OPTIONS nstxout = 0; No output, except for last frame (coordinates) nstvout = 0; No output, except for last frame (velocities) nstfout = 0; No output, except for last frame (forces) nstlog = 50; Write every step to the log nstenergy= 50; Write energies at every step xtc_grps = Protein nstxtcout= 50; Do not write a compressed trajectory energygrps = Protein Non-Protein ; Write energy information separately for these groups ; NEIGHBORSEARCHING PARAMETERS nstlist = 5 ns-type = Grid pbc = xyz rlist= 2.0 ; OPTIONS FOR ELECTROSTATICS AND VDW coulombtype = Reaction-field-zero rcoulomb = 1.8 epsilon_rf = 0 vdw-type = Switch rvdw = 2.0 rvdw-switch = 1.6 Well, here's the problem. Read about proper usage of the switch function, especially the note about the size of rlist: http://manual.gromacs.org/current/online/mdp_opt.html#vdw -Justin ; Spacing for the PME/PPPM FFT fourierspacing = 0.12 ; 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= 4 ewald_rtol = 1e-05 epsilon_surface = 0 optimize_fft = no ; Temperature coupling tcoupl = nose-hoover tc-grps = Protein Non-Protein tau_t= 0.2 0.2 ref_t= 300 300 ; Pressure coupling pcoupl = no ; OPTIONS FOR BONDS constraints = all-bonds constraint-algorithm = SHAKE shake_tol= 0.0001 Pooja
Re: [gmx-users] Charge grps and cut-off
A charge grp consisting of 12 atoms is created from Arginine residues in my topology file. ; residue 14 ARG rtp ARG q +1.0 476NH1 14ARG N150 -0.47 14.007 ; qtot -3.47 477 H 14ARG HN150 0.31 1.008 ; qtot -3.16 478CT1 14ARG CA150 0.07 12.011 ; qtot -3.09 479 HB 14ARG HA150 0.09 1.008 ; qtot -3 480CT2 14ARG CB151 -0.18 12.011 ; qtot -3.18 481 HA 14ARGHB1151 0.09 1.008 ; qtot -3.09 482 HA 14ARGHB2151 0.09 1.008 ; qtot -3 483CT2 14ARG CG152 -0.18 12.011 ; qtot -3.18 484 HA 14ARGHG1152 0.09 1.008 ; qtot -3.09 485 HA 14ARGHG2152 0.09 1.008 ; qtot -3 486CT2 14ARG CD1530.2 12.011 ; qtot -2.8 487 HA 14ARGHD1153 0.09 1.008 ; qtot -2.71 488 HA 14ARGHD2153 0.09 1.008 ; qtot -2.62 489NC2 14ARG NE153 -0.7 14.007 ; qtot -3.32 490 HC 14ARG HE153 0.44 1.008 ; qtot -2.88 491 C 14ARG CZ153 0.64 12.011 ; qtot -2.24 492NC2 14ARGNH1153 -0.8 14.007 ; qtot -3.04 493 HC 14ARG HH11153 0.46 1.008 ; qtot -2.58 494 HC 14ARG HH12153 0.46 1.008 ; qtot -2.12 495NC2 14ARGNH2153 -0.8 14.007 ; qtot -2.92 496 HC 14ARG HH21153 0.46 1.008 ; qtot -2.46 497 HC 14ARG HH22153 0.46 1.008 ; qtot -2 498 C 14ARG C154 0.51 12.011 ; qtot -1.49 499 O 14ARG O154 -0.51 15.999 ; qtot -2 See charge group 153. It has 12 atoms. This is true for all Arginine residues. It seems that charge groups must have an integer net-charge. As you can see, it assigns charge grps 151, 152, 153 etc. till the net-charge becomes an integer. One option would be to manually make them. In this case, I could simply breakdown this particular charge grp into 2 smaller chargegrps but I am sure if that would be consistent with the forcefield and not sure if it would be possible to set the net charge to an integral value to an integer for the smaller charge groups. Also, is there an alternate way by changing the Cut-off? Any thoughts? Pooja Pooja -- 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] Charge grps and cut-off
This is the arginine entry in the rtp file. It assigns 12 atoms to charge grp 3. [ ARG ] [ atoms ] N NH1 -0.47 0 HN H 0.310 CA CT1 0.070 HA HB 0.090 CB CT2 -0.18 1 HB1 HA 0.091 HB2 HA 0.091 CG CT2 -0.18 2 HG1 HA 0.092 HG2 HA 0.092 CD CT2 0.203 HD1 HA 0.093 HD2 HA 0.093 NE NC2 -0.70 3 HE HC 0.443 CZ C 0.643 NH1 NC2 -0.80 3 HH11HC 0.463 HH12HC 0.463 NH2 NC2 -0.80 3 HH21HC 0.463 HH22HC 0.463 C C 0.514 O O -0.51 4 On Sat, Jul 17, 2010 at 9:17 AM, Sai Pooja saipo...@gmail.com wrote: A charge grp consisting of 12 atoms is created from Arginine residues in my topology file. ; residue 14 ARG rtp ARG q +1.0 476NH1 14ARG N150 -0.47 14.007 ; qtot -3.47 477 H 14ARG HN150 0.31 1.008 ; qtot -3.16 478CT1 14ARG CA150 0.07 12.011 ; qtot -3.09 479 HB 14ARG HA150 0.09 1.008 ; qtot -3 480CT2 14ARG CB151 -0.18 12.011 ; qtot -3.18 481 HA 14ARGHB1151 0.09 1.008 ; qtot -3.09 482 HA 14ARGHB2151 0.09 1.008 ; qtot -3 483CT2 14ARG CG152 -0.18 12.011 ; qtot -3.18 484 HA 14ARGHG1152 0.09 1.008 ; qtot -3.09 485 HA 14ARGHG2152 0.09 1.008 ; qtot -3 486CT2 14ARG CD1530.2 12.011 ; qtot -2.8 487 HA 14ARGHD1153 0.09 1.008 ; qtot -2.71 488 HA 14ARGHD2153 0.09 1.008 ; qtot -2.62 489NC2 14ARG NE153 -0.7 14.007 ; qtot -3.32 490 HC 14ARG HE153 0.44 1.008 ; qtot -2.88 491 C 14ARG CZ153 0.64 12.011 ; qtot -2.24 492NC2 14ARGNH1153 -0.8 14.007 ; qtot -3.04 493 HC 14ARG HH11153 0.46 1.008 ; qtot -2.58 494 HC 14ARG HH12153 0.46 1.008 ; qtot -2.12 495NC2 14ARGNH2153 -0.8 14.007 ; qtot -2.92 496 HC 14ARG HH21153 0.46 1.008 ; qtot -2.46 497 HC 14ARG HH22153 0.46 1.008 ; qtot -2 498 C 14ARG C154 0.51 12.011 ; qtot -1.49 499 O 14ARG O154 -0.51 15.999 ; qtot -2 See charge group 153. It has 12 atoms. This is true for all Arginine residues. It seems that charge groups must have an integer net-charge. As you can see, it assigns charge grps 151, 152, 153 etc. till the net-charge becomes an integer. One option would be to manually make them. In this case, I could simply breakdown this particular charge grp into 2 smaller chargegrps but I am sure if that would be consistent with the forcefield and not sure if it would be possible to set the net charge to an integral value to an integer for the smaller charge groups. Also, is there an alternate way by changing the Cut-off? Any thoughts? Pooja Pooja -- Quaerendo Invenietis-Seek and you shall discover. -- 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] Charge grps and cut-off
Sai Pooja wrote: A charge grp consisting of 12 atoms is created from Arginine residues in my topology file. ; residue 14 ARG rtp ARG q +1.0 476NH1 14ARG N150 -0.47 14.007 ; qtot -3.47 477 H 14ARG HN150 0.31 1.008 ; qtot -3.16 478CT1 14ARG CA150 0.07 12.011 ; qtot -3.09 479 HB 14ARG HA150 0.09 1.008 ; qtot -3 480CT2 14ARG CB151 -0.18 12.011 ; qtot -3.18 481 HA 14ARGHB1151 0.09 1.008 ; qtot -3.09 482 HA 14ARGHB2151 0.09 1.008 ; qtot -3 483CT2 14ARG CG152 -0.18 12.011 ; qtot -3.18 484 HA 14ARGHG1152 0.09 1.008 ; qtot -3.09 485 HA 14ARGHG2152 0.09 1.008 ; qtot -3 486CT2 14ARG CD1530.2 12.011 ; qtot -2.8 487 HA 14ARGHD1153 0.09 1.008 ; qtot -2.71 488 HA 14ARGHD2153 0.09 1.008 ; qtot -2.62 489NC2 14ARG NE153 -0.7 14.007 ; qtot -3.32 490 HC 14ARG HE153 0.44 1.008 ; qtot -2.88 491 C 14ARG CZ153 0.64 12.011 ; qtot -2.24 492NC2 14ARGNH1153 -0.8 14.007 ; qtot -3.04 493 HC 14ARG HH11153 0.46 1.008 ; qtot -2.58 494 HC 14ARG HH12153 0.46 1.008 ; qtot -2.12 495NC2 14ARGNH2153 -0.8 14.007 ; qtot -2.92 496 HC 14ARG HH21153 0.46 1.008 ; qtot -2.46 497 HC 14ARG HH22153 0.46 1.008 ; qtot -2 498 C 14ARG C154 0.51 12.011 ; qtot -1.49 499 O 14ARG O154 -0.51 15.999 ; qtot -2 See charge group 153. It has 12 atoms. This is true for all Arginine residues. It seems that charge groups must have an integer net-charge. As you can see, it assigns charge grps 151, 152, 153 etc. till the net-charge becomes an integer. Strictly speaking, charge groups do not always have to have a net charge, but generally they do. One option would be to manually make them. In this case, I could simply breakdown this particular charge grp into 2 smaller chargegrps but I am sure if that would be consistent with the forcefield and not sure if it would be possible to set the net charge to an integral value to an integer for the smaller charge groups. Simply breaking the charge group apart seems too arbitrary. If you're not using PME (which you're not), then you need integral charge groups, so it looks like this one has to stay intact. It just seems like there's the potential for inaccurate short-range interactions when the entire sidechain is encompassed by a single charge group. Perhaps for your case it will not matter so much; maybe someone else can comment. There are numerous threads in the list archive discussing this situation, so I won't repeat all of that here. Also, is there an alternate way by changing the Cut-off? Not really. Any cutoff you choose might be affected by artifacts of a large charge group. -Justin Any thoughts? Pooja Pooja -- 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 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] Charge grps and cut-off
Hi, So if I use PME for coloumb interactions, then what are my options? Would you then suggest breaking up the 12-atom charge grp in the arginine residue into 2 charge groups? Would it be enough to make the changes in the .rtp or parameters in other files must be changed? POoja On Sat, Jul 17, 2010 at 11:16 AM, Justin A. Lemkul jalem...@vt.edu wrote: Sai Pooja wrote: A charge grp consisting of 12 atoms is created from Arginine residues in my topology file. ; residue 14 ARG rtp ARG q +1.0 476NH1 14ARG N150 -0.47 14.007 ; qtot -3.47 477 H 14ARG HN150 0.31 1.008 ; qtot -3.16 478CT1 14ARG CA150 0.07 12.011 ; qtot -3.09 479 HB 14ARG HA150 0.09 1.008 ; qtot -3 480CT2 14ARG CB151 -0.18 12.011 ; qtot -3.18481 HA 14ARGHB1151 0.09 1.008 ; qtot -3.09 482 HA 14ARGHB2151 0.09 1.008 ; qtot -3 483CT2 14ARG CG152 -0.18 12.011 ; qtot -3.18484 HA 14ARGHG1152 0.09 1.008 ; qtot -3.09485 HA 14ARGHG2152 0.09 1.008 ; qtot -3 486CT2 14ARG CD 1530.2 12.011 ; qtot -2.8 487 HA 14ARG HD1153 0.09 1.008 ; qtot -2.71 488 HA 14ARGHD2153 0.09 1.008 ; qtot -2.62 489NC2 14ARG NE153 -0.7 14.007 ; qtot -3.32 490 HC 14ARG HE153 0.44 1.008 ; qtot -2.88 491 C 14ARG CZ153 0.64 12.011 ; qtot -2.24 492NC2 14ARGNH1153 -0.8 14.007 ; qtot -3.04 493 HC 14ARG HH11153 0.46 1.008 ; qtot -2.58 494 HC 14ARG HH12153 0.46 1.008 ; qtot -2.12 495NC2 14ARGNH2153 -0.8 14.007 ; qtot -2.92 496 HC 14ARG HH21153 0.46 1.008 ; qtot -2.46 497 HC 14ARG HH22153 0.46 1.008 ; qtot -2 498 C 14ARG C154 0.51 12.011 ; qtot -1.49 499 O 14ARG O154 -0.51 15.999 ; qtot -2 See charge group 153. It has 12 atoms. This is true for all Arginine residues. It seems that charge groups must have an integer net-charge. As you can see, it assigns charge grps 151, 152, 153 etc. till the net-charge becomes an integer. Strictly speaking, charge groups do not always have to have a net charge, but generally they do. One option would be to manually make them. In this case, I could simply breakdown this particular charge grp into 2 smaller chargegrps but I am sure if that would be consistent with the forcefield and not sure if it would be possible to set the net charge to an integral value to an integer for the smaller charge groups. Simply breaking the charge group apart seems too arbitrary. If you're not using PME (which you're not), then you need integral charge groups, so it looks like this one has to stay intact. It just seems like there's the potential for inaccurate short-range interactions when the entire sidechain is encompassed by a single charge group. Perhaps for your case it will not matter so much; maybe someone else can comment. There are numerous threads in the list archive discussing this situation, so I won't repeat all of that here. Also, is there an alternate way by changing the Cut-off? Not really. Any cutoff you choose might be affected by artifacts of a large charge group. -Justin Any thoughts? Pooja Pooja -- 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 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 -- Quaerendo Invenietis-Seek and you shall discover. -- 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
[gmx-users] pull code example
Hi all, Could anybody please share some working system to look at the pull code in gromacs? I did not find any examples in the WWW, unfortunately. Vitaly -- Dr. Vitaly Chaban -- 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] Need For a Script
Hey,.. Thank you for the script. I will keep in mind what you said next time. Samrat Pal From: Justin A. Lemkul jalem...@vt.edu To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Fri, July 16, 2010 5:18:44 PM Subject: Re: [gmx-users] Need For a Script Samrat Pal wrote: Dear All, I am a new GROMACS user. I have been able to solvate a protein in a water box and also to simulate it and unfold it by heating it. But I have facing problem with the script of AFM pulling. I want to unfold a protein by pulling the two ends of the protein. Can anyone give me a full script for that so that I can standardise my protocol? Suggestion is urgent. http://www.gromacs.org/Documentation/Tutorials#Umbrella_Sampling Also, as a bit of advice, don't use the word urgent when asking for free help. You're hoping someone else (who is busy) will find time to solve an issue for you. -Justin Thanks in advance Samrat Pal -- 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 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 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] g_rmsf
Hi, I am running an npt simulation for a protein in water. For more than 50% of the residues the backbone atoms have been restrained by applying posrestraints. I ran g_rmsf to check if the pos-restraints were working well. When I do this selecting 'backbone' from the groups menu, my rmsf file gives 'nan' for certain residues: # This file was created Sat Jul 17 13:40:21 2010 # by the following command: # ../../gromacsnew/bin/g_rmsf -f npt1.cpt -s npt1.tpr -b 0 -e 80 -o rmsf2_npt1.xvg -od rmsd2_npt1.xvg -res # # g_rmsf is part of G R O M A C S: # # GROup of MAchos and Cynical Suckers # @title RMS fluctuation @xaxis label Residue @yaxis label (nm) @TYPE xy 1 nan 2 nan 3 0.0002 4 0. 5 nan 1 0.0002 2 nan 3 nan 4 0.0001 5 nan 6 0.0001 7 nan 8 nan 9 0. 10 0.0002 11 nan 12 nan 13 nan 14 nan 15 0. 16 nan 17 0.0001 18 0.0002 Does this mean that the simulations are not working properly? Does this problem occur frequently due to the way the simulation parameters haev been set? Pooja -- Quaerendo Invenietis-Seek and you shall discover. -- 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] (no subject)
Hi, I am studying polyglutamine regarding to my Ph.D work. Now my sequence is NH3+ -Q-Q-Q-Q-Q-Q-Q-Q-Q-Q-Q-Q-COO-. I would like to cap the N and C terminal with the protecting groups CH3CO and NHCH3 instead of NH3+ and COO- respectively (i.e. CH3CONH-Q-Q-Q-Q-Q-CONHCH3). I am using GROMACS software for this study. I have tried with GROMACS but its library has not been included with N Acety and N Methylamide at its N and C terminal. Due to this .gro file or .top file could not be made. I have even included the CH3CO group in the library. still it is not making sense to produce the .gro and .top file. I request you to suggest how to cap the above thereby to overcome this problem using GROMACS. M. Baskar, Dept of Biophysics, Panjab University, Chandigarh, India. -- 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] g_rmsf
Hi Pooja, Try to get a grip on the file types and what they contain. A .cpt file is a checkpoint file containing a single configuration. Not much fluctuation to expect there. This sort of analysis only makes sense for a trajectory, or at least an ensemble of structures. Try the .xtc or the .trr file. Cheers, Tsjerk On Sat, Jul 17, 2010 at 7:55 PM, Sai Pooja saipo...@gmail.com wrote: Hi, I am running an npt simulation for a protein in water. For more than 50% of the residues the backbone atoms have been restrained by applying posrestraints. I ran g_rmsf to check if the pos-restraints were working well. When I do this selecting 'backbone' from the groups menu, my rmsf file gives 'nan' for certain residues: # This file was created Sat Jul 17 13:40:21 2010 # by the following command: # ../../gromacsnew/bin/g_rmsf -f npt1.cpt -s npt1.tpr -b 0 -e 80 -o rmsf2_npt1.xvg -od rmsd2_npt1.xvg -res # # g_rmsf is part of G R O M A C S: # # GROup of MAchos and Cynical Suckers # @ title RMS fluctuation @ xaxis label Residue @ yaxis label (nm) @TYPE xy 1 nan 2 nan 3 0.0002 4 0. 5 nan 1 0.0002 2 nan 3 nan 4 0.0001 5 nan 6 0.0001 7 nan 8 nan 9 0. 10 0.0002 11 nan 12 nan 13 nan 14 nan 15 0. 16 nan 17 0.0001 18 0.0002 Does this mean that the simulations are not working properly? Does this problem occur frequently due to the way the simulation parameters haev been set? Pooja -- Quaerendo Invenietis-Seek and you shall discover. -- gmx-users mailing list gmx-us...@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 -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group Groningen Institute for Biomolecular Research and Biotechnology University of Groningen The Netherlands -- 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] g_sas for martini coarse-grained particles
Hi, I am trying to estimate the solvent accessible surface area of hydrophobic tails of a martini DPPC lipid bilayer . I was going to use g_sas for that. But, I observe that this tool gets the vanderwal radii from vdwradii.dat file. But, since the particles in the martini lipids are united-atom types, I was wondering what will be a reasonable radius to use for hydrophobic tail particles of a martini lipid ? Thanks Sanku -- 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] pull code example
I'd send a list of links except that the other end of a google search for gromacs pull code example has all of what you will need to broaden your general pull code understanding. The mailing list has an absolutely massive number of posts on this too. Chris. Hi all, Could anybody please share some working system to look at the pull code in gromacs? I did not find any examples in the WWW, unfortunately. Vitaly -- Dr. Vitaly Chaban -- 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] gromacs-localp-3.0.2 installation problem
Hi all, Hi all I tried to install gromacs-localp-3.0.2 on Fedora 11. First, I successfully run ./configure: …….. …….. config.status: creating man/Makefile config.status: creating man/man1/Makefile config.status: creating src/config.h GROMACS / LOCALPRESSURE is ready to compile. * Binaries and libraries for this host will be installed in /usr/local/gromacs-localp/i686-pc-linux-gnu/bin /usr/local/gromacs-localp/i686-pc-linux-gnu/lib and shared data will placed in /usr/local/gromacs-localp/share (You can set this with --prefix, --exec-prefix and --datadir) * You are compiling a double precision version of the package - program names will be suffixed with _d to avoid overwriting single precision files. You can override it with --program-suffix But after making make-distclean followed by make command, I am facing this error message: ………. ……… cc -DHAVE_CONFIG_H -I. -I. -I../../src -I../../include -DGMXLIBDIR=\/usr/local/gromacs-localp/share/top\ -O6 -fomit-frame-pointer -finline-functions -Wall -Wno-unused -malign-double -funroll-all-loops -o mkinl mkinl.o mkinl_declarations.o mkinl_outerloop.o mkinl_innerloop.o mkinl_calcdist.o mkinl_invsqrt.o mkinl_recip.o mkinl_interactions.o metacode.o ./mkinl c This is the GROMACS innerloop code generator It will generate double precision C code in file innerc.c Using gromacs invsqrt code Inlining gromacs invsqrt and/or reciprocal code Using normal solvent optimized loops Prefetching coordinates in loops: none Prefetching forces in loops: none Nonthreaded inner loops Vectorizing invsqrt in loops:none Progress: 1% Progress: 2% Progress: 3% Progress: 5% Progress: 6% Progress: 7% Progress: 8% Progress: 10% Progress: 11% Progress: 12% Progress: 14% Progress: 15% Progress: 16% Progress: 17% Progress: 19% Progress: 20% Progress: 21% Progress: 23% Progress: 24% Progress: 25% Progress: 26% Progress: 28% Progress: 29% Progress: 30% Progress: 32% Progress: 33% Progress: 34% Progress: 35% Progress: 37% Progress: 38% Progress: 39% Progress: 41% Progress: 42% Progress: 43% Progress: 44% Progress: 46% Progress: 47% Progress: 48% Progress: 50% Progress: 51% Progress: 52% Progress: 53% Progress: 55% Progress: 56% Progress: 57% Progress: 58% Progress: 60% Progress: 61% Progress: 62% Progress: 64% Progress: 65% Progress: 66% Progress: 67% Progress: 69% Progress: 70% Progress: 71% Progress: 73% Progress: 74% Progress: 75% Progress: 76% Progress: 78% Progress: 79% Progress: 80% Progress: 82% Progress: 83% Progress: 84% Progress: 85% Progress: 87% Progress: 88% Progress: 89% Progress: 91% Progress: 92% Progress: 93% Progress: 94% Progress: 96% Progress: 97% Progress: 98% Progress: 100% Generated 29303 lines of code in 78 functions (innerc.c may take a while to compile) source='innerc.c' object='innerc.lo' libtool=yes \ depfile='.deps/innerc.Plo' tmpdepfile='.deps/innerc.TPlo' \ depmode=gcc3 /bin/sh ../../config/depcomp \ /bin/sh ../../libtool --mode=compile cc -DHAVE_CONFIG_H -I. -I. -I../../src -I../../include -DGMXLIBDIR=\/usr/local/gromacs-localp/share/top\ -O6 -fomit-frame-pointer -finline-functions -Wall -Wno-unused -malign-double -funroll-all-loops -c -o innerc.lo `test -f innerc.c || echo './'`innerc.c cc -DHAVE_CONFIG_H -I. -I. -I../../src -I../../include -DGMXLIBDIR=\/usr/local/gromacs-localp/share/top\ -O6 -fomit-frame-pointer -finline-functions -Wall -Wno-unused -malign-double -funroll-all-loops -c innerc.c -MT innerc.lo -MD -MP -MF .deps/innerc.TPlo -o innerc.o In file included from ../../include/typedefs.h:53, from innerc.c:8: ../../include/sysstuff.h:46:2: warning: #ident is a deprecated GCC extension In file included from ../../include/types/graph.h:40, from ../../include/typedefs.h:66, from innerc.c:8: ../../include/fatal.h:46:2: warning: #ident is a deprecated GCC extension In file included from ../../include/vec.h:100, from innerc.c:10: ../../include/maths.h:46:2: warning: #ident is a deprecated GCC extension In file included from ../../include/vec.h:103, from innerc.c:10: ../../include/macros.h:46:2: warning: #ident is a deprecated GCC extension innerc.c:25018:7: error: invalid suffix a on integer constant innerc.c: In function 'inl3302': innerc.c:25018: error: expected ';' before ')' token innerc.c:25018: error: expected statement before ')' token innerc.c:25018: error: expected expression before '=' token innerc.c:27591:7: error: invalid suffix a on integer constant innerc.c: In function 'inl3402': innerc.c:27591: error: expected ';' before ')' token innerc.c:27591: error: expected statement before ')' token innerc.c:27591: error: expected expression before '=' token make[3]: *** [innerc.lo] Error 1 make[3]: Leaving directory
