[gmx-users] C36 parameters for POPG
Hi, Anybody knows where can I get the charmm36 parameters for POPG? I couldn't find it in lipidbook. Has it been produced by any users? Thanks in advance. Sincerely, Shima -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] LINCS WARNING - Protein-Membrane-system
Hi, I have a system of Peptide-popc-ions-water to simulate. I'm trying to run MD simulation following the Justin's tutorial of kalp15-DPPC. The force field which I use, is charmm36. In NVT step, I get LINCS-warning as follow: Step 0, time 0 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 2.460224, max 54.696251 (between atoms 4719 and 4716) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length Step 0, time 0 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.182707, max 15.613569 (between atoms 4725 and 4726) When I checked the warning, I see the first warning is related to 2 atoms of 71POPC, the chain of 71POPC residue is broken near these two atoms. And the other warning is related to a bond between H and C in the other POPC residue. Some settings of nvt.mdp is as: ns_type = grid nstlist = 5 rlist = 1.2 rlistlong = 1.4 rcoulomb = 1.2 rvdw = 1.2 pbc = xyz vdwtype = switch rvdw_switch = 0.8 ; Parameters for treating bonded interactions continuation = no constraint_algorithm = LINCS constraints = all-bonds lincs_iter = 1 lincs_order = 4 Do I need to increase the rlistlong? I have done a simulation of POPC-water before with these settings, but everything was ok. So what's the problem? Anybody may help me? Your suggestions would be appreciated. Thanks in advance. Sincerely, Shima -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] LINCS WARNING - Protein-Membrane-system
On 1/1/13 8:56 AM, Shima Arasteh wrote: Hi, I have a system of Peptide-popc-ions-water to simulate. I'm trying to run MD simulation following the Justin's tutorial of kalp15-DPPC. The force field which I use, is charmm36. In NVT step, I get LINCS-warning as follow: Step 0, time 0 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 2.460224, max 54.696251 (between atoms 4719 and 4716) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length Step 0, time 0 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.182707, max 15.613569 (between atoms 4725 and 4726) When I checked the warning, I see the first warning is related to 2 atoms of 71POPC, the chain of 71POPC residue is broken near these two atoms. And the other warning is related to a bond between H and C in the other POPC residue. Some settings of nvt.mdp is as: ns_type= grid nstlist= 5 rlist= 1.2 rlistlong = 1.4 rcoulomb= 1.2 rvdw= 1.2 pbc= xyz vdwtype = switch rvdw_switch = 0.8 ; Parameters for treating bonded interactions continuation= no constraint_algorithm = LINCS constraints= all-bonds lincs_iter= 1 lincs_order= 4 Do I need to increase the rlistlong? I have done a simulation of POPC-water before with these settings, but everything was ok. So what's the problem? Anybody may help me? Don't haphazardly mess with cutoffs. Doing so usually makes your problem worse. Think about it scientifically - if POPC/water worked fine, but a POPC/protein/water system doesn't, what's the variable that changed? Moreover, look at when the failure is happening - it's failing at step zero. LINCS warnings always have the same causes: 1. Wrong .mdp settings (likely not the case, see above) 2. Insufficient equilibration (well, yours is failing outright, so probably not) 3. Insufficient minimization (hmmm...) -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] LINCS WARNING - Protein-Membrane-system
Thanks. I compared settings of mdp files in POPC/WATER and POPC/PROTEIN/WATER systems. The only difference I found between them was about the bonds constraints. The constraints of mdp file for POPC/WATER was constraints = h-bonds , however it was constraints = all-bonds for POPC/PROTEIN/WATER system. You say insufficient minimization, I don't think so . I got a sensible potential energy as follow: Potential Energy = -1.2414742e+06 Maximum force = 9.8055229e+01 on atom 4719 Norm of force = 3.4904923e+00 Then what's wrong with the EM? Sincerely, Shima - Original Message - From: Justin Lemkul jalem...@vt.edu To: Shima Arasteh shima_arasteh2...@yahoo.com; Discussion list for GROMACS users gmx-users@gromacs.org Cc: Sent: Tuesday, January 1, 2013 6:45 PM Subject: Re: [gmx-users] LINCS WARNING - Protein-Membrane-system On 1/1/13 8:56 AM, Shima Arasteh wrote: Hi, I have a system of Peptide-popc-ions-water to simulate. I'm trying to run MD simulation following the Justin's tutorial of kalp15-DPPC. The force field which I use, is charmm36. In NVT step, I get LINCS-warning as follow: Step 0, time 0 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 2.460224, max 54.696251 (between atoms 4719 and 4716) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length Step 0, time 0 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.182707, max 15.613569 (between atoms 4725 and 4726) When I checked the warning, I see the first warning is related to 2 atoms of 71POPC, the chain of 71POPC residue is broken near these two atoms. And the other warning is related to a bond between H and C in the other POPC residue. Some settings of nvt.mdp is as: ns_type = grid nstlist = 5 rlist = 1.2 rlistlong = 1.4 rcoulomb = 1.2 rvdw = 1.2 pbc = xyz vdwtype = switch rvdw_switch = 0.8 ; Parameters for treating bonded interactions continuation = no constraint_algorithm = LINCS constraints = all-bonds lincs_iter = 1 lincs_order = 4 Do I need to increase the rlistlong? I have done a simulation of POPC-water before with these settings, but everything was ok. So what's the problem? Anybody may help me? Don't haphazardly mess with cutoffs. Doing so usually makes your problem worse. Think about it scientifically - if POPC/water worked fine, but a POPC/protein/water system doesn't, what's the variable that changed? Moreover, look at when the failure is happening - it's failing at step zero. LINCS warnings always have the same causes: 1. Wrong .mdp settings (likely not the case, see above) 2. Insufficient equilibration (well, yours is failing outright, so probably not) 3. Insufficient minimization (hmmm...) -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] LINCS WARNING - Protein-Membrane-system
On 1/1/13 10:41 AM, Shima Arasteh wrote: Thanks. I compared settings of mdp files in POPC/WATER and POPC/PROTEIN/WATER systems. The only difference I found between them was about the bonds constraints. The constraints of mdp file for POPC/WATER was constraints = h-bonds , however it was constraints = all-bonds for POPC/PROTEIN/WATER system. You say insufficient minimization, I don't think so . I got a sensible potential energy as follow: Potential Energy = -1.2414742e+06 Maximum force = 9.8055229e+01 on atom 4719 Norm of force = 3.4904923e+00 Then what's wrong with the EM? Please post a complete .mdp file for both the EM and NVT processes. Without that information, it's pure guesswork. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Index file
I used genconf and got a new gro file. Then I saw the ions are not recognized because of the same numbering of ions with last SOL molecules. Therefore, I changed them manually, so the problem was solved. Thanks for your suggestions dear Justin. Happy New Year! Sincerely, Shima - Original Message - From: Justin Lemkul jalem...@vt.edu To: Shima Arasteh shima_arasteh2...@yahoo.com Cc: Sent: Monday, December 31, 2012 8:37 PM Subject: Re: [gmx-users] Index file On 12/31/12 11:58 AM, Shima Arasteh wrote: These are the last line of my gro file: 5SOL HW299818 7.429 8.372 11.524 5CL CL99819 0.485 3.864 11.451 5CL CL99820 5.689 6.730 9.692 9.21490 8.92980 12.40750 Here, I brought you the output of make_ndx command. As you see CL ions are not recognized here. Analysing residue names: There are: 48 Protein residues There are: 238 Other residues There are: 12624 Water residues Analysing Protein... Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 0 System : 99817 atoms 1 Protein : 720 atoms 2 Protein-H : 356 atoms 3 C-alpha : 48 atoms 4 Backbone : 144 atoms 5 MainChain : 190 atoms 6 MainChain+Cb : 234 atoms 7 MainChain+H : 240 atoms 8 SideChain : 480 atoms 9 SideChain-H : 166 atoms 10 Prot-Masses : 720 atoms 11 non-Protein : 99097 atoms 12 Other : 31892 atoms 13 POPC : 31892 atoms 14 Water : 67205 atoms 15 SOL : 67205 atoms 16 non-Water : 32612 atoms nr : group ! 'name' nr name 'splitch' nr Enter: list groups 'a': atom 'del' nr 'splitres' nr 'l': list residues 't': atom type | 'keep' nr 'splitat' nr 'h': help 'r': residue 'res' nr 'chain' char name: group 'case': case sensitive 'q': save and quit 'ri': residue index Somehow confusing for me! It could be that both your last SOL and both CL ions have the same residue number. Renumber the file with genconf and try again. The only other thing I can think of is that you don't have an entry for CL in residuetypes.dat indicating that it is an ion. The Ion group should be generated by default whenever an ion is encountered, but you don't have one. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] LINCS WARNING - Protein-Membrane-system
If I tell you that I changed the constraints and now the NVT is running, would that be ok? However I don't know the scientific reason of this incident! But I bring you the EM.mdp as follow: define = -DSTRONG_POSRES integrator = steep ; Algorithm (steep = steepest descent minimization) emtol = 100.0 ; Stop minimization when the maximum force 100.0 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 = 1.2 ; Cut-off for making neighbor list (short range forces) coulombtype = PME ; Treatment of long range electrostatic interactions rcoulomb = 1.2 ; Short-range electrostatic cut-off rvdw = 1.2 ; Short-range Van der Waals cut-off pbc = xyz ; Periodic Boundary Conditions And the NVT.mdp as follow (after change of all-bond constraint to h-bond): title = NVT equilibration for dimer-POPC - CHARMM36 define = -DPOSRES ; Protein is position restrained (uses the posres.itp file information) ; Parameters describing the details of the NVT simulation protocol integrator = md ; Algorithm (md = molecular dynamics [leap-frog integrator]; md-vv = md using velocity verlet; sd = stochastic dynamics) dt = 0.002 ; Time-step (ps) nsteps = 5 ; Number of steps to run (0.002 * 5 = 100 ps) ; Parameters controlling output writing nstxout = 1 ; Write coordinates to output .trr file every 2 ps nstvout = 1000 ; Write velocities to output .trr file every 2 ps nstenergy = 1000 ; Write energies to output .edr file every 2 ps nstlog = 1000 ; Write output to .log file every 2 ps ; Parameters describing neighbors searching and details about interaction calculations ns_type = grid ; Neighbor list search method (simple, grid) nstlist = 5 ; Neighbor list update frequency (after every given number of steps) rlist = 1.2 ; Neighbor list search cut-off distance (nm) rlistlong = 1.4 rcoulomb = 1.2 ; Short-range Coulombic interactions cut-off distance (nm) rvdw = 1.2 ; Short-range van der Waals cutoff distance (nm) pbc = xyz ; Direction in which to use Perodic Boundary Conditions (xyz, xy, no) vdwtype = switch rvdw_switch = 0.8 ; Parameters for treating bonded interactions continuation = no ; Whether a fresh start or a continuation from a previous run (yes/no) constraint_algorithm = LINCS ; Constraint algorithm (LINCS / SHAKE) constraints = h-bonds ; Which bonds/angles to constrain (all-bonds / hbonds / none / all-angles / h-angles) lincs_iter = 1 ; Number of iterations to correct for rotational lengthening in LINCS (related to accuracy) lincs_order = 4 ; Highest order in the expansion of the constraint coupling matrix (related to accuracy) ; Parameters for treating electrostatic interactions coulombtype = PME ; Long range electrostatic interactions treatment (cut-off, Ewald, PME) pme_order = 4 ; Interpolation order for PME (cubic interpolation is represented by 4) fourierspacing = 0.16 ; Maximum grid spacing for FFT grid using PME (nm) ; Temperature coupling parameters tcoupl = v-rescale ; Modified Berendsen thermostat using velocity rescaling tc-grps = Protein POPC SOL_CL ; Define groups to be coupled separately to temperature bath tau_t = 0.1 0.1 0.1 ; Group-wise coupling time constant (ps) ref_t = 310 310 310 ; Group-wise reference temperature (K) ; Pressure coupling parameters pcoupl = no ; Under NVT conditions pressure coupling is not done ; Miscellaneous control parameters ; Dispersion correction DispCorr = EnerPres ; Dispersion corrections for Energy and Pressure for vdW cut-off ; Initial Velocity Generation gen_vel = yes ; Generate velocities from Maxwell distribution at given temperature gen_temp = 310 ; Specific temperature for Maxwell distribution (K) gen_seed = -1 ; Use random seed for velocity generation (integer; -1 means seed is calculated from the process ID number) ; Centre of mass (COM) motion removal relative to the specified groups nstcomm = 1 ; COM removal frequency (steps) comm_mode = Linear ; Remove COM translation (linear / angular / no) comm_grps = Protein_POPC SOL_CL ; COM removal relative to the specified groups Any suggestions please? Sincerely, Shima - Original Message - From: Justin
Re: [gmx-users] LINCS WARNING - Protein-Membrane-system
On 1/1/13 10:53 AM, Shima Arasteh wrote: If I tell you that I changed the constraints and now the NVT is running, would that be ok? However I don't know the scientific reason of this incident! But I bring you the EM.mdp as follow: define = -DSTRONG_POSRES integrator= steep; Algorithm (steep = steepest descent minimization) emtol= 100.0 ; Stop minimization when the maximum force 100.0 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= 1.2; Cut-off for making neighbor list (short range forces) coulombtype= PME; Treatment of long range electrostatic interactions rcoulomb= 1.2; Short-range electrostatic cut-off rvdw= 1.2; Short-range Van der Waals cut-off pbc= xyz ; Periodic Boundary Conditions And the NVT.mdp as follow (after change of all-bond constraint to h-bond): title= NVT equilibration for dimer-POPC - CHARMM36 define= -DPOSRES; Protein is position restrained (uses the posres.itp file information) ; Parameters describing the details of the NVT simulation protocol integrator= md; Algorithm (md = molecular dynamics [leap-frog integrator]; md-vv = md using velocity verlet; sd = stochastic dynamics) dt= 0.002; Time-step (ps) nsteps= 5; Number of steps to run (0.002 * 5 = 100 ps) ; Parameters controlling output writing nstxout= 1; Write coordinates to output .trr file every 2 ps nstvout= 1000; Write velocities to output .trr file every 2 ps nstenergy= 1000; Write energies to output .edr file every 2 ps nstlog= 1000; Write output to .log file every 2 ps ; Parameters describing neighbors searching and details about interaction calculations ns_type= grid; Neighbor list search method (simple, grid) nstlist= 5; Neighbor list update frequency (after every given number of steps) rlist= 1.2; Neighbor list search cut-off distance (nm) rlistlong = 1.4 rcoulomb= 1.2; Short-range Coulombic interactions cut-off distance (nm) rvdw= 1.2; Short-range van der Waals cutoff distance (nm) pbc= xyz; Direction in which to use Perodic Boundary Conditions (xyz, xy, no) vdwtype = switch rvdw_switch = 0.8 ; Parameters for treating bonded interactions continuation= no; Whether a fresh start or a continuation from a previous run (yes/no) constraint_algorithm = LINCS; Constraint algorithm (LINCS / SHAKE) constraints= h-bonds ; Which bonds/angles to constrain (all-bonds / hbonds / none / all-angles / h-angles) lincs_iter= 1; Number of iterations to correct for rotational lengthening in LINCS (related to accuracy) lincs_order= 4; Highest order in the expansion of the constraint coupling matrix (related to accuracy) ; Parameters for treating electrostatic interactions coulombtype= PME; Long range electrostatic interactions treatment (cut-off, Ewald, PME) pme_order= 4; Interpolation order for PME (cubic interpolation is represented by 4) fourierspacing= 0.16; Maximum grid spacing for FFT grid using PME (nm) ; Temperature coupling parameters tcoupl= v-rescale; Modified Berendsen thermostat using velocity rescaling tc-grps= Protein POPCSOL_CL; Define groups to be coupled separately to temperature bath tau_t= 0.10.10.1; Group-wise coupling time constant (ps) ref_t= 310 310310; Group-wise reference temperature (K) ; Pressure coupling parameters pcoupl= no ; Under NVT conditions pressure coupling is not done ; Miscellaneous control parameters ; Dispersion correction DispCorr= EnerPres; Dispersion corrections for Energy and Pressure for vdW cut-off ; Initial Velocity Generation gen_vel= yes; Generate velocities from Maxwell distribution at given temperature gen_temp= 310; Specific temperature for Maxwell distribution (K) gen_seed= -1; Use random seed for velocity generation (integer; -1 means seed is calculated from the process ID number) ; Centre of mass (COM) motion removal relative to the specified groups nstcomm= 1; COM removal frequency (steps) comm_mode= Linear; Remove COM translation (linear / angular / no) comm_grps= Protein_POPC SOL_CL; COM removal relative to the specified groups Any suggestions please? Yes, the
Re: [gmx-users] LINCS WARNING - Protein-Membrane-system
Thanks. Sincerely, Shima - Original Message - From: Justin Lemkul jalem...@vt.edu To: Shima Arasteh shima_arasteh2...@yahoo.com; Discussion list for GROMACS users gmx-users@gromacs.org Cc: Sent: Tuesday, January 1, 2013 7:27 PM Subject: Re: [gmx-users] LINCS WARNING - Protein-Membrane-system On 1/1/13 10:53 AM, Shima Arasteh wrote: If I tell you that I changed the constraints and now the NVT is running, would that be ok? However I don't know the scientific reason of this incident! But I bring you the EM.mdp as follow: define = -DSTRONG_POSRES integrator = steep ; Algorithm (steep = steepest descent minimization) emtol = 100.0 ; Stop minimization when the maximum force 100.0 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 = 1.2 ; Cut-off for making neighbor list (short range forces) coulombtype = PME ; Treatment of long range electrostatic interactions rcoulomb = 1.2 ; Short-range electrostatic cut-off rvdw = 1.2 ; Short-range Van der Waals cut-off pbc = xyz ; Periodic Boundary Conditions And the NVT.mdp as follow (after change of all-bond constraint to h-bond): title = NVT equilibration for dimer-POPC - CHARMM36 define = -DPOSRES ; Protein is position restrained (uses the posres.itp file information) ; Parameters describing the details of the NVT simulation protocol integrator = md ; Algorithm (md = molecular dynamics [leap-frog integrator]; md-vv = md using velocity verlet; sd = stochastic dynamics) dt = 0.002 ; Time-step (ps) nsteps = 5 ; Number of steps to run (0.002 * 5 = 100 ps) ; Parameters controlling output writing nstxout = 1 ; Write coordinates to output .trr file every 2 ps nstvout = 1000 ; Write velocities to output .trr file every 2 ps nstenergy = 1000 ; Write energies to output .edr file every 2 ps nstlog = 1000 ; Write output to .log file every 2 ps ; Parameters describing neighbors searching and details about interaction calculations ns_type = grid ; Neighbor list search method (simple, grid) nstlist = 5 ; Neighbor list update frequency (after every given number of steps) rlist = 1.2 ; Neighbor list search cut-off distance (nm) rlistlong = 1.4 rcoulomb = 1.2 ; Short-range Coulombic interactions cut-off distance (nm) rvdw = 1.2 ; Short-range van der Waals cutoff distance (nm) pbc = xyz ; Direction in which to use Perodic Boundary Conditions (xyz, xy, no) vdwtype = switch rvdw_switch = 0.8 ; Parameters for treating bonded interactions continuation = no ; Whether a fresh start or a continuation from a previous run (yes/no) constraint_algorithm = LINCS ; Constraint algorithm (LINCS / SHAKE) constraints = h-bonds ; Which bonds/angles to constrain (all-bonds / hbonds / none / all-angles / h-angles) lincs_iter = 1 ; Number of iterations to correct for rotational lengthening in LINCS (related to accuracy) lincs_order = 4 ; Highest order in the expansion of the constraint coupling matrix (related to accuracy) ; Parameters for treating electrostatic interactions coulombtype = PME ; Long range electrostatic interactions treatment (cut-off, Ewald, PME) pme_order = 4 ; Interpolation order for PME (cubic interpolation is represented by 4) fourierspacing = 0.16 ; Maximum grid spacing for FFT grid using PME (nm) ; Temperature coupling parameters tcoupl = v-rescale ; Modified Berendsen thermostat using velocity rescaling tc-grps = Protein POPC SOL_CL ; Define groups to be coupled separately to temperature bath tau_t = 0.1 0.1 0.1 ; Group-wise coupling time constant (ps) ref_t = 310 310 310 ; Group-wise reference temperature (K) ; Pressure coupling parameters pcoupl = no ; Under NVT conditions pressure coupling is not done ; Miscellaneous control parameters ; Dispersion correction DispCorr = EnerPres ; Dispersion corrections for Energy and Pressure for vdW cut-off ; Initial Velocity Generation gen_vel = yes ; Generate velocities from Maxwell distribution at given temperature gen_temp = 310 ; Specific temperature for Maxwell distribution (K) gen_seed = -1 ; Use random seed for velocity generation
[gmx-users] GB parameter(s) missing or negative but they aint missing nor negative
Dear all, Im trying to run an md or em using an implicit solvation method using gromacs 4.5.5 but I allways get the same errors. GB parameter(s) missing or negative for atom type 'OS' GB parameter(s) missing or negative for atom type 'H2' GB parameter(s) missing or negative for atom type 'N*' GB parameter(s) missing or negative for atom type 'CK' GB parameter(s) missing or negative for atom type 'P' --- Program grompp, VERSION 4.5.5 Source code file: grompp.c, line: 1123 Fatal error: Can't do GB electrostatics; the implicit_genborn_params section of the forcefield is missing parameters for 5 atomtypes or they might be negative. Istart from default.pdb (41bp RNA) and perform following: pdb2gmx -f default.pdb -ff amber03 -water none -ignh editconf -f conf.gro -d 2 -bt triclinic -c grompp -f em_gbis.mdp -c out.gro with em_gbis.mdp containing: integrator= steep nsteps= -1 nstlist= 10 emstep=1 rlist= 2.0 coulombtype= cut-off rcoulomb= 2.0 vdw-type= cut-off rvdw= 2.0 nstenergy= 10 implicit_solvent = GBSA constraints=none rgbradii=2.0 gb_algorithm=OBC sa_algorithm=Ace-approximation Now the odd part is that I added all missing parameters to the /gromacs-4.5.5/share/top/amber...ff/gbsa.itp for example for H2: ... H4 0.1 1 10.115 0.85 ; H H5 0.1 1 10.125 0.85 ; H H2 0.1 1 10.125 0.85 ; H ... I tried doing this for amber 94, 99 and 03 but allways the same result. Anyone got a clue? I dont think I did something wrong as the implicit solvation model previously worked. All input is appreciated. Thanks in advance, Gert -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] GB parameter(s) missing or negative but they aint missing nor negative
On 1/1/13 1:31 PM, Gert Peters wrote: Dear all, Im trying to run an md or em using an implicit solvation method using gromacs 4.5.5 but I allways get the same errors. GB parameter(s) missing or negative for atom type 'OS' GB parameter(s) missing or negative for atom type 'H2' GB parameter(s) missing or negative for atom type 'N*' GB parameter(s) missing or negative for atom type 'CK' GB parameter(s) missing or negative for atom type 'P' --- Program grompp, VERSION 4.5.5 Source code file: grompp.c, line: 1123 Fatal error: Can't do GB electrostatics; the implicit_genborn_params section of the forcefield is missing parameters for 5 atomtypes or they might be negative. Istart from default.pdb (41bp RNA) and perform following: pdb2gmx -f default.pdb -ff amber03 -water none -ignh editconf -f conf.gro -d 2 -bt triclinic -c grompp -f em_gbis.mdp -c out.gro with em_gbis.mdp containing: integrator= steep nsteps= -1 nstlist= 10 emstep=1 rlist= 2.0 coulombtype= cut-off rcoulomb= 2.0 vdw-type= cut-off rvdw= 2.0 nstenergy= 10 implicit_solvent = GBSA constraints=none rgbradii=2.0 gb_algorithm=OBC sa_algorithm=Ace-approximation Now the odd part is that I added all missing parameters to the /gromacs-4.5.5/share/top/amber...ff/gbsa.itp for example for H2: ... H4 0.1 1 10.115 0.85 ; H H5 0.1 1 10.125 0.85 ; H H2 0.1 1 10.125 0.85 ; H ... I tried doing this for amber 94, 99 and 03 but allways the same result. Anyone got a clue? I dont think I did something wrong as the implicit solvation model previously worked. All input is appreciated. From the path you've written above, it seems to imply you are modifying the gbsa.itp file in the source rather than the actual installed version. Is that the case? If so, are you editing it prior to installation? That's the only way it will work, otherwise you need to make the changes in the amber03.ff subdirectory in $GMXLIB (/path/to/your/gromacs/share/gromacs/top). -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re: Simulation of 2D lattice model
Have someone else any ideas how the topology for a simple 2D lattice could be done ?:) I've tried to build it manually but for the system of 48 nodes definition of the angles and impropers have appeared very routinely :( James 2012/12/30, James Starlight jmsstarli...@gmail.com: Hi Leandro! Actually I need such model of simple 2D lattice for study of the hessian matrix. So I'd like to perform simulation of very simple system without any rotation freedoms and calculate eigenvectors from that trajectory by means of Esential dynamics analysis. Than I'd like to watch on what exactly principal components different motions would be observed. Finally I'd like to calculate normal modes from different MD snapshots and compare different sub-spaces with the EDA results. So any aproximate system for such task would be suitable (I've decided to use lattice because it's most simple that I've imagine ). By the way I supose that such topology coupld be eaasily done from topology of fullerene :) But I've lack it too. James 2012/12/30 Leandro Bortot leandro@gmail.com: Leandro -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] secondary structure analyze
On 1/1/13 2:06 PM, Parisa Rahmani wrote: Hi gmx users I want to do secondary structure analyze for my trajectory of protein. I've downloaded DSSP packages from ftp://ftp.cmbi.ru.nl/pub/software/dssp/dssp-2.0.4.tgz; and put it in /usr/local/bin , and rename the folder to dssp. when i run do_dssp -f rmsd.pdb -s protein.tpr -sc scount.xvg -o ss.xpm the following appears, Opening library file /home/parisa/parisa/share/gromacs/top/phbres.dat Opening library file /home/parisa/parisa/share/gromacs/top/aminoacids.dat Group 0 ( System) has 420 elements Group 1 ( Protein) has 420 elements Group 2 ( Protein-H) has 322 elements Group 3 ( C-alpha) has43 elements Group 4 (Backbone) has 128 elements Group 5 ( MainChain) has 171 elements Group 6 (MainChain+Cb) has 208 elements Group 7 ( MainChain+H) has 214 elements Group 8 ( SideChain) has 206 elements Group 9 ( SideChain-H) has 150 elements Select a group: 1 Selected 1: 'Protein' There are 43 residues in your selected group Opening library file /home/parisa/parisa/share/gromacs/top/ss.map Reading frame 0 time1.000 Back Off! I just backed up dd35REJx to ./#dd35REJx.1# and the program is continuously running without .xpm and xvg outputs. i searched the mailing list, but I couldn't find the solution (because many of them was about the old DSSP version , that is not available now) any suggestion would be greatly appreciated. do_dssp is very slow. The output files are only produced at the very end, when the program is done running. For some of my longer trajectories, the program runs for a few hours. It all depends on how many frames you have to analyze. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re: Simulation of 2D lattice model
On 1/1/13 2:01 PM, James Starlight wrote: Have someone else any ideas how the topology for a simple 2D lattice could be done ?:) I've tried to build it manually but for the system of 48 nodes definition of the angles and impropers have appeared very routinely :( For regularly spaced atoms, g_x2top should do it. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] secondary structure analyze
Thanks Justin for the reply, how i can sure that it uses the DSSP package correctly , it seems that it just uses the gromacs code : ( Opening library file /home/parisa/parisa/share/gromacs/top/phbres.dat Opening library file /home/parisa/parisa/share/gromacs/top/aminoacids.dat Opening library file /home/parisa/parisa/share/**gromacs/top/ss.map ) for some reasons I use gromacs 3.3.3. On Tue, Jan 1, 2013 at 10:39 PM, Justin Lemkul jalem...@vt.edu wrote: On 1/1/13 2:06 PM, Parisa Rahmani wrote: Hi gmx users I want to do secondary structure analyze for my trajectory of protein. I've downloaded DSSP packages from ftp://ftp.cmbi.ru.nl/pub/**software/dssp/dssp-2.0.4.tgzftp://ftp.cmbi.ru.nl/pub/software/dssp/dssp-2.0.4.tgz and put it in /usr/local/bin , and rename the folder to dssp. when i run do_dssp -f rmsd.pdb -s protein.tpr -sc scount.xvg -o ss.xpm the following appears, Opening library file /home/parisa/parisa/share/**gromacs/top/phbres.dat Opening library file /home/parisa/parisa/share/** gromacs/top/aminoacids.dat Group 0 ( System) has 420 elements Group 1 ( Protein) has 420 elements Group 2 ( Protein-H) has 322 elements Group 3 ( C-alpha) has43 elements Group 4 (Backbone) has 128 elements Group 5 ( MainChain) has 171 elements Group 6 (MainChain+Cb) has 208 elements Group 7 ( MainChain+H) has 214 elements Group 8 ( SideChain) has 206 elements Group 9 ( SideChain-H) has 150 elements Select a group: 1 Selected 1: 'Protein' There are 43 residues in your selected group Opening library file /home/parisa/parisa/share/**gromacs/top/ss.map Reading frame 0 time1.000 Back Off! I just backed up dd35REJx to ./#dd35REJx.1# and the program is continuously running without .xpm and xvg outputs. i searched the mailing list, but I couldn't find the solution (because many of them was about the old DSSP version , that is not available now) any suggestion would be greatly appreciated. do_dssp is very slow. The output files are only produced at the very end, when the program is done running. For some of my longer trajectories, the program runs for a few hours. It all depends on how many frames you have to analyze. -Justin -- ==**== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] secondary structure analyze
On 1/1/13 2:17 PM, Parisa Rahmani wrote: Thanks Justin for the reply, how i can sure that it uses the DSSP package correctly , it seems that it just uses the gromacs code : ( Opening library file /home/parisa/parisa/share/gromacs/top/phbres.dat Opening library file /home/parisa/parisa/share/gromacs/top/aminoacids.dat Opening library file /home/parisa/parisa/share/**gromacs/top/ss.map ) for some reasons I use gromacs 3.3.3. The do_dssp program is simply a wrapper that runs the (external) dssp executable on every frame in the trajectory. Gromacs has several definitions it uses for various properties of the different residues, so that's what you see it opening. If there are no errors, it is running correctly. Failures are rather obvious by design. -Justin On Tue, Jan 1, 2013 at 10:39 PM, Justin Lemkul jalem...@vt.edu wrote: On 1/1/13 2:06 PM, Parisa Rahmani wrote: Hi gmx users I want to do secondary structure analyze for my trajectory of protein. I've downloaded DSSP packages from ftp://ftp.cmbi.ru.nl/pub/**software/dssp/dssp-2.0.4.tgzftp://ftp.cmbi.ru.nl/pub/software/dssp/dssp-2.0.4.tgz and put it in /usr/local/bin , and rename the folder to dssp. when i run do_dssp -f rmsd.pdb -s protein.tpr -sc scount.xvg -o ss.xpm the following appears, Opening library file /home/parisa/parisa/share/**gromacs/top/phbres.dat Opening library file /home/parisa/parisa/share/** gromacs/top/aminoacids.dat Group 0 ( System) has 420 elements Group 1 ( Protein) has 420 elements Group 2 ( Protein-H) has 322 elements Group 3 ( C-alpha) has43 elements Group 4 (Backbone) has 128 elements Group 5 ( MainChain) has 171 elements Group 6 (MainChain+Cb) has 208 elements Group 7 ( MainChain+H) has 214 elements Group 8 ( SideChain) has 206 elements Group 9 ( SideChain-H) has 150 elements Select a group: 1 Selected 1: 'Protein' There are 43 residues in your selected group Opening library file /home/parisa/parisa/share/**gromacs/top/ss.map Reading frame 0 time1.000 Back Off! I just backed up dd35REJx to ./#dd35REJx.1# and the program is continuously running without .xpm and xvg outputs. i searched the mailing list, but I couldn't find the solution (because many of them was about the old DSSP version , that is not available now) any suggestion would be greatly appreciated. do_dssp is very slow. The output files are only produced at the very end, when the program is done running. For some of my longer trajectories, the program runs for a few hours. It all depends on how many frames you have to analyze. -Justin -- ==**== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- Justin A. Lemkul, Ph.D. Research Scientist 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/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Re: GB parameter(s) missing or negative but they aint missing nor negative
Justin Lemkul wrote On 1/1/13 1:31 PM, Gert Peters wrote: Anyone got a clue? I dont think I did something wrong as the implicit solvation model previously worked. All input is appreciated. From the path you've written above, it seems to imply you are modifying the gbsa.itp file in the source rather than the actual installed version. Is that the case? If so, are you editing it prior to installation? That's the only way it will work, otherwise you need to make the changes in the amber03.ff subdirectory in $GMXLIB (/path/to/your/gromacs/share/gromacs/top). -Justin You're absolutely right. Thank you very much. Stupid mistake. Greetings, Gert -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing list gmx-users@ http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-request@ . * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- View this message in context: http://gromacs.5086.n6.nabble.com/GB-parameter-s-missing-or-negative-but-they-aint-missing-nor-negative-tp5004164p5004172.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Linear CG beads, grompp doesn't work
Dear advanced gromac users, I am trying to simulate a long linear chain of polymer using CG beads. (about 200 beads), all with same type charge interactions. (examples shown:) I read on previous gromacs mailing list that linear systems with same charges make the system unstable? But is there anyway to go around that? [atoms] 1 P3 O1 mon 1 0.00 2 P3 O1 mon 2 0.00 3 P3 O1 mon 3 0.00 4 P3 O1 mon 4 0.00 5 P3 O1 mon 5 0.00 6 P3 O1 mon 6 0.00 7 P3 O1 mon 7 0.00 8 P3 O1 mon 8 0.00 9 P3 O1 mon 9 0.00 ……. [ bonds ] 1 2 1 0.4317000 2 3 1 0.4317000 3 4 1 0.4317000 4 5 1 0.4317000 …… However, when i do grompp -f vac_min.mdp -c mon.gro -p mon.top -o vac.tpr -it returns the error of: Fatal error: The largest charge group contains 200 atoms. The maximum is 32. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors Please let me know if there is a way to go around that. Thank you. Xu Dong Huang Chemical Biochemical Engineering Rutgers School of Engineering xudo...@eden.rutgers.edu -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Linear CG beads, grompp doesn't work
On 1/1/13 10:33 PM, Xu Dong Huang wrote: Dear advanced gromac users, I am trying to simulate a long linear chain of polymer using CG beads. (about 200 beads), all with same type charge interactions. (examples shown:) I read on previous gromacs mailing list that linear systems with same charges make the system unstable? But is there anyway to go around that? It's the angles that make the system unstable. One can use virtual sites to get around the issue. There is a trivial example in a tutorial I wrote: http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/vsites/index.html The bigger question is whether or not the angles in the molecule impose linearity, or whether the initial configuration is simply a line of particles that may deviate according to angle and dihedral potentials. You haven't shown the [angles] or [dihedrals] directives, so it's not clear what you're intending, exactly. [atoms] 1 P3 O1 mon 1 0.00 2 P3 O1 mon 2 0.00 3 P3 O1 mon 3 0.00 4 P3 O1 mon 4 0.00 5 P3 O1 mon 5 0.00 6 P3 O1 mon 6 0.00 7 P3 O1 mon 7 0.00 8 P3 O1 mon 8 0.00 9 P3 O1 mon 9 0.00 ……. [ bonds ] 1 2 1 0.4317000 2 3 1 0.4317000 3 4 1 0.4317000 4 5 1 0.4317000 …… However, when i do grompp -f vac_min.mdp -c mon.gro -p mon.top -o vac.tpr -it returns the error of: Fatal error: The largest charge group contains 200 atoms. The maximum is 32. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors Please let me know if there is a way to go around that. Thank you. Do as the error message says and put fewer than 32 atoms in each charge group. The size of the charge group has implications for neighbor searching if using a group-based cutoff scheme. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Linear CG beads, grompp doesn't work
Dear Justin, My .itp does not contain angles or dihedrals because we are simply interested in the very simple generic case of a linear (what we assume by defining a coordinate file of linear beads) polymer model. I will go through the tutorial and try to see if it resolves my issue. Xu Dong Huang Chemical Biochemical Engineering Rutgers School of Engineering xudo...@eden.rutgers.edu On Jan 1, 2013, at 10:38 PM, Justin Lemkul jalem...@vt.edu wrote: On 1/1/13 10:33 PM, Xu Dong Huang wrote: Dear advanced gromac users, I am trying to simulate a long linear chain of polymer using CG beads. (about 200 beads), all with same type charge interactions. (examples shown:) I read on previous gromacs mailing list that linear systems with same charges make the system unstable? But is there anyway to go around that? It's the angles that make the system unstable. One can use virtual sites to get around the issue. There is a trivial example in a tutorial I wrote: http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/vsites/index.html The bigger question is whether or not the angles in the molecule impose linearity, or whether the initial configuration is simply a line of particles that may deviate according to angle and dihedral potentials. You haven't shown the [angles] or [dihedrals] directives, so it's not clear what you're intending, exactly. [atoms] 1P3 O1 mon 1 0.00 2P3 O1 mon 2 0.00 3P3 O1 mon 3 0.00 4P3 O1 mon 4 0.00 5P3 O1 mon 5 0.00 6P3 O1 mon 6 0.00 7P3 O1 mon 7 0.00 8P3 O1 mon 8 0.00 9P3 O1 mon 9 0.00 ……. [ bonds ] 12 1 0.4317000 23 1 0.4317000 34 1 0.4317000 45 1 0.4317000 …… However, when i do grompp -f vac_min.mdp -c mon.gro -p mon.top -o vac.tpr -it returns the error of: Fatal error: The largest charge group contains 200 atoms. The maximum is 32. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors Please let me know if there is a way to go around that. Thank you. Do as the error message says and put fewer than 32 atoms in each charge group. The size of the charge group has implications for neighbor searching if using a group-based cutoff scheme. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] RE: gmx-users Digest, Vol 105, Issue 5
First of all Happy New Year to everyone. Second, Justin I admire you. You keep this forum alive and very well tended. Great job.Third, Parisa, try running do_dssp with the flag -dt and pick an interval one or two orders of magnitude smaller than the length of your simulation. That should do it. Best regards. Message: 7 Date: Tue, 1 Jan 2013 22:47:39 +0330 From: Parisa Rahmani rahmani.p...@gmail.com Subject: Re: [gmx-users] secondary structure analyze To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: caac4-tstt+pgwo04avj64hflvkz8mnsqrf-uugykbuxcs5r...@mail.gmail.com Content-Type: text/plain; charset=ISO-8859-1 Thanks Justin for the reply, how i can sure that it uses the DSSP package correctly , it seems that it just uses the gromacs code : ( Opening library file /home/parisa/parisa/share/gromacs/top/phbres.dat Opening library file /home/parisa/parisa/share/gromacs/top/aminoacids.dat Opening library file /home/parisa/parisa/share/**gromacs/top/ss.map ) for some reasons I use gromacs 3.3.3. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Linear CG beads, grompp doesn't work
On 1/1/13 10:46 PM, Xu Dong Huang wrote: Dear Justin, My .itp does not contain angles or dihedrals because we are simply interested in the very simple generic case of a linear (what we assume by defining a coordinate file of linear beads) polymer model. I will go through the tutorial and try to see if it resolves my issue. The molecule will not remain linear simply due to consecutive bonds. Hopefully the tutorial explains some of the necessary methodology for creating species that are indeed to be kept linear, though the example therein (CO2) is considerably less complex than what you seek to do. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Linear CG beads, grompp doesn't work
@Justin, Does the philosophy described in your tutorial apply to CG martini bead models where 1 bead describes the entire CO2 atom? (If I were to do that, assuming) Xu Dong Huang Chemical Biochemical Engineering Rutgers School of Engineering xudo...@eden.rutgers.edu On Jan 1, 2013, at 10:46 PM, Xu Dong Huang xudo...@eden.rutgers.edu wrote: Dear Justin, My .itp does not contain angles or dihedrals because we are simply interested in the very simple generic case of a linear (what we assume by defining a coordinate file of linear beads) polymer model. I will go through the tutorial and try to see if it resolves my issue. Xu Dong Huang Chemical Biochemical Engineering Rutgers School of Engineering xudo...@eden.rutgers.edu On Jan 1, 2013, at 10:38 PM, Justin Lemkul jalem...@vt.edu wrote: On 1/1/13 10:33 PM, Xu Dong Huang wrote: Dear advanced gromac users, I am trying to simulate a long linear chain of polymer using CG beads. (about 200 beads), all with same type charge interactions. (examples shown:) I read on previous gromacs mailing list that linear systems with same charges make the system unstable? But is there anyway to go around that? It's the angles that make the system unstable. One can use virtual sites to get around the issue. There is a trivial example in a tutorial I wrote: http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/vsites/index.html The bigger question is whether or not the angles in the molecule impose linearity, or whether the initial configuration is simply a line of particles that may deviate according to angle and dihedral potentials. You haven't shown the [angles] or [dihedrals] directives, so it's not clear what you're intending, exactly. [atoms] 1 P3 O1 mon 1 0.00 2 P3 O1 mon 2 0.00 3 P3 O1 mon 3 0.00 4 P3 O1 mon 4 0.00 5 P3 O1 mon 5 0.00 6 P3 O1 mon 6 0.00 7 P3 O1 mon 7 0.00 8 P3 O1 mon 8 0.00 9 P3 O1 mon 9 0.00 ……. [ bonds ] 1 2 1 0.4317000 2 3 1 0.4317000 3 4 1 0.4317000 4 5 1 0.4317000 …… However, when i do grompp -f vac_min.mdp -c mon.gro -p mon.top -o vac.tpr -it returns the error of: Fatal error: The largest charge group contains 200 atoms. The maximum is 32. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors Please let me know if there is a way to go around that. Thank you. Do as the error message says and put fewer than 32 atoms in each charge group. The size of the charge group has implications for neighbor searching if using a group-based cutoff scheme. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Linear CG beads, grompp doesn't work
On 1/1/13 10:51 PM, Xu Dong Huang wrote: @Justin, Does the philosophy described in your tutorial apply to CG martini bead models where 1 bead describes the entire CO2 atom? (If I were to do that, assuming) Presumably. As long as you satisfy the criteria mentioned in the tutorial (moment of inertia and total mass), you should be able to get it to work. I've never dealt with polymers and have very little personal experience with CG models, so I don't know if there are other methodological issues that one might encounter. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Electric field GROMACS
Dear GROMACS users, A couple of days back I posted an issue which I have been facing, I request you all to kindly help me.. I posted the following issue: I ran a simulation using E_x as 1, 0.002, 0 i.e. i wanted a 0.002 V/nm electric field strength. The simulation completed successfully. But now i am confused with fact that the electric field which i subjected my sample to was STATIC or OSCILLATING. I presume it to be static as i didn't include any frequency value in the mdp file for the electric field (Am i correct?) How can i include an oscillating electric field code in the mdp file. We are trying to use Gromacs for the first time. I hope i can get some guidance and help. Can someone please help me with the code to include the external electric field (STATIC AND OSCILLATING). PLEASE... Regards Ash -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Umbrella sampling - regd
On 1/1/13 11:48 PM, ramesh cheerla wrote: Dear Gromacs users, I am performing umbrella sampling simulations by selecting configurations with spacing window of 0.02nm from pulling simulations with the following options in .mdp file to get PMF along a axis for permeation of ion through a channel. ; Pull code pull= umbrella pull_geometry = position ; simple distance increase pull_dim = N Y N pull_vec1= 0 -1 0 pull_start = yes ; define initial COM distance 0 pull_ngroups= 1 pull_group0 = FIXEDATOM pull_group1 = SMDATOM pull_rate1 = 0.0 ; 0.01 nm per ps = 10 nm per ns pull_k1 = 2000 ; kJ mol^-1 nm^-2 pull_init1 = 0 And am using g_wham to get PMF, while using g_wham, am getting the warnings like : WARNING, no data point in bin 139 (z=-0.492557) ! You may not get a reasonable profile. Check your histograms! Warning, poor sampling bin 193 (z=-0.364322). Check your histograms! Warning, poor sampling bin 194 (z=-0.361947). Check your histograms! Warning, poor sampling bin 195 (z=-0.359572). Check your histograms! Warning, poor sampling bin 196 (z=-0.357197). Check your histograms! Warning, poor sampling bin 197 (z=-0.354823). Check your histograms! Warning, poor sampling bin 198 (z=-0.352448). Check your histograms! Warning, poor sampling bin 199 (z=-0.350073). Check your histograms! Initialized rapid wham stuff (contrib tolerance 6.7e-08) Evaluating only 2115 of 3000 expressions. I have checked my histograms and PMF profile, by doing so I have understood that histograms overlapping is restricted to only some regions and there is no histograms at all in some regions i.e severe sampling problems at barrier regions. here I am sending the link that containing PMF profile that I have obtained, http://researchweb.iiit.ac.in/~bipin.singh/pmf.jpg Can anybody tell me how can I get proper sampling at barrier regions is there any efficient way to do this, how about meta dynamics with suitable CV (collective variable) ? . Use a stronger force constant in these barrier regions to restrict the movement along the reaction coordinate. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Umbrella sampling - regd
Dear Justin, Thank you very much for your quick reply. Regards, Ramesh. On Wed, Jan 2, 2013 at 10:24 AM, Justin Lemkul jalem...@vt.edu wrote: On 1/1/13 11:48 PM, ramesh cheerla wrote: Dear Gromacs users, I am performing umbrella sampling simulations by selecting configurations with spacing window of 0.02nm from pulling simulations with the following options in .mdp file to get PMF along a axis for permeation of ion through a channel. ; Pull code pull= umbrella pull_geometry = position ; simple distance increase pull_dim = N Y N pull_vec1= 0 -1 0 pull_start = yes ; define initial COM distance 0 pull_ngroups= 1 pull_group0 = FIXEDATOM pull_group1 = SMDATOM pull_rate1 = 0.0 ; 0.01 nm per ps = 10 nm per ns pull_k1 = 2000 ; kJ mol^-1 nm^-2 pull_init1 = 0 And am using g_wham to get PMF, while using g_wham, am getting the warnings like : WARNING, no data point in bin 139 (z=-0.492557) ! You may not get a reasonable profile. Check your histograms! Warning, poor sampling bin 193 (z=-0.364322). Check your histograms! Warning, poor sampling bin 194 (z=-0.361947). Check your histograms! Warning, poor sampling bin 195 (z=-0.359572). Check your histograms! Warning, poor sampling bin 196 (z=-0.357197). Check your histograms! Warning, poor sampling bin 197 (z=-0.354823). Check your histograms! Warning, poor sampling bin 198 (z=-0.352448). Check your histograms! Warning, poor sampling bin 199 (z=-0.350073). Check your histograms! Initialized rapid wham stuff (contrib tolerance 6.7e-08) Evaluating only 2115 of 3000 expressions. I have checked my histograms and PMF profile, by doing so I have understood that histograms overlapping is restricted to only some regions and there is no histograms at all in some regions i.e severe sampling problems at barrier regions. here I am sending the link that containing PMF profile that I have obtained, http://researchweb.iiit.ac.in/** ~bipin.singh/pmf.jpg http://researchweb.iiit.ac.in/~bipin.singh/pmf.jpg Can anybody tell me how can I get proper sampling at barrier regions is there any efficient way to do this, how about meta dynamics with suitable CV (collective variable) ? . Use a stronger force constant in these barrier regions to restrict the movement along the reaction coordinate. -Justin -- ==**== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
