[gmx-users] Hessian matrix within gmx mdrun
Hello, I'm trying to do a normal modes analysis on a large crystalline system (~100,000 atoms of MgO). I expected the hessian to be (300,000x300,000), or NDIM*natoms, but by poking around in the source code a *little*, I can see that the Hessian is made only by the atom types, not by the actual atoms. Is there a way to do it based on individual atoms? I've tried looking for examples on how to do this, but all the links I can find to details are broken. Thanks, Adriaan Riet -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Invalid order for directive atomtypes for ligands
On 6/28/18 4:19 PM, Qasim Pars wrote: Dear users, I have a protein bound to two different ligands. LIG1.itp and LIG2.itp files of both ligands include [ atomtypes ] part. I get "Invalid order for directive atomtypes" error while running energy minimization step. Do I have to combine [ atomtypes ] parts of both ligands to get rid of this error? Yes. All parameters must be defined before any molecules can be declared. http://www.gromacs.org/Documentation/Errors?highlight=errors#Invalid_order_for_directive_xxx -Justin Here is top file of the system: #include "/amber99sb-ildn.ff/forcefield.itp" #include "Protein_chain_A.itp" #include "Protein_chain_B.itp" #include "/amber99sb-ildn.ff/tip3p.itp" #ifdef POSRES_WATER ; Position restraint for each water oxygen [ position_restraints ] ; i funct fcxfcyfcz 11 1000 1000 1000 #endif #include "/amber99sb-ildn.ff/ions.itp" #include "LIG1.itp" #ifdef POSRES #include "posre_LIG1.itp" #endif #include "LIG2.itp" #ifdef POSRES #include "posre_LIG2.itp" #endif [ system ] Protein in water [ molecules ] ; Compound#mols Protein_chain_A 1 Protein_chain_B 1 LIG1 1 LIG2 1 SOL16018 Thanks in advance -- == Justin A. Lemkul, Ph.D. Assistant Professor Virginia Tech Department of Biochemistry 303 Engel Hall 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.thelemkullab.com == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Invalid order for directive atomtypes for ligands
Dear users, I have a protein bound to two different ligands. LIG1.itp and LIG2.itp files of both ligands include [ atomtypes ] part. I get "Invalid order for directive atomtypes" error while running energy minimization step. Do I have to combine [ atomtypes ] parts of both ligands to get rid of this error? Here is top file of the system: #include "/amber99sb-ildn.ff/forcefield.itp" #include "Protein_chain_A.itp" #include "Protein_chain_B.itp" #include "/amber99sb-ildn.ff/tip3p.itp" #ifdef POSRES_WATER ; Position restraint for each water oxygen [ position_restraints ] ; i funct fcxfcyfcz 11 1000 1000 1000 #endif #include "/amber99sb-ildn.ff/ions.itp" #include "LIG1.itp" #ifdef POSRES #include "posre_LIG1.itp" #endif #include "LIG2.itp" #ifdef POSRES #include "posre_LIG2.itp" #endif [ system ] Protein in water [ molecules ] ; Compound#mols Protein_chain_A 1 Protein_chain_B 1 LIG1 1 LIG2 1 SOL16018 Thanks in advance -- Qasim Pars -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Potential energy reported by gmx energy command
Den 2018-06-28 kl. 09:03, skrev atb files: Hello experts, I did a LJ particles simulation, where I simulated two systems, 100 particle and 400 particle. For 100 particles energy is: Energy Average Err.Est. RMSD Tot-Drift --- Potential 0.126288 0.029 0.615731 -0.0324041 (kJ/mol) Kinetic En. 337.039 0.24 27.6568 0.443176 (kJ/mol) Total Energy 337.165 0.22 27.6615 0.410771 (kJ/mol) For 400 particle energy is: Energy Average Err.Est. RMSD Tot-Drift --- Potential 0.502517 0.042 1.34584 0.220501 (kJ/mol) Kinetic En. 1359 0.82 56.1468 -1.24836 (kJ/mol) Total Energy 1359.5 0.78 56.1548 -1.02787 (kJ/mol) Since both systems have exact same operating conditions, only particle number has been changed, the per particle energy should be same, right? Here I see the energies has become 4 times in the second case. Then what is meaning of reporting energies in "KJ/mol" ? There is nothing like my system is not fully equilibrated, I have thoroughly checked, the both systems are well equilibrated. Please help in understanding these energies. Thank you gmx energy does not know what your system is composed of. However the -nmol 400 flag may help. -- David van der Spoel, Ph.D., Professor of Biology Head of Department, Cell & Molecular Biology, Uppsala University. Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205. http://www.icm.uu.se -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Use different version of tpr in the same simulation... possible ?
On 6/28/18 10:17 AM, ABEL Stephane wrote: Hi there For different reason, I have to use a different version of GROMACS (GMX2016.4) to continue a simulation carried out with GROMACS v2018. Obvioulsy I obtain an error appears about the tpr "reading tpx file version 112 with version 110 program" Is there an alternative to do what I want ? Re-create the .tpr file with 2016.4. GROMACS versions are not backwards-compatible. -Justin -- == Justin A. Lemkul, Ph.D. Assistant Professor Virginia Tech Department of Biochemistry 303 Engel Hall 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.thelemkullab.com == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Use different version of tpr in the same simulation... possible ?
Hi there For different reason, I have to use a different version of GROMACS (GMX2016.4) to continue a simulation carried out with GROMACS v2018. Obvioulsy I obtain an error appears about the tpr "reading tpx file version 112 with version 110 program" Is there an alternative to do what I want ? Thank you -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Umbrella sampling
Hi, I do umbrella sampling for different distances of AA along surface and i calculated error by bootstrapping method. Error is less than 0.5 kj.mol-1 in 0.8to1.7 nm far from surface, but in 0.6to0.8 nm error is about 2 kj.mol-1 . The minimum energy is about -5kj.mol-1 at 0.65 nm. All windows overlapped in histo plot. So how should i know that this error is neglectable or not? I did sampling many times but near surface, the error is too much and windows have significant overlapping and count is about 2 times higher than 0.8 to 1.7 nm. Would you please help me? Is there any criteria other than overlapping and estimating error i should notice to? -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Fwd: Ionic liquid and CNTs
Thanks a lot ! I'm going to do it straight away ... I'll let you know the results ! Thanks ever so much ! Candy 2018-06-28 9:43 GMT+02:00 Alex : > Ah, that's a scary looking system. :) > > Indeed, there are vacuum pockets, because the system has not been brought > to correct pressure. All you have to do for your relaxation run is use a > semiisotropic barostat (maybe Berendsen, but only for relaxation) with a > realistic solvent compressibility in the Z-direction and zero > compressibility in the XY-plane. Gromacs allows this rather easily. And run > it for something like 5-10 ns, not 0.5 ns. > > Alex > > > > On 6/28/2018 1:30 AM, Candy Deck wrote: > >> Hi Alex, >> Thanks for your answer ... >> Here is the pdb file of my system : https://files.fm/u/7crt2yd5 >> Candy >> >> 2018-06-27 22:30 GMT+02:00 Alex : >> >> If there is a bubble, all it could mean is that the volume simply too >>> large, which could be expected, given the combination of short simulation >>> and low compressibility. It is also unclear what your system looks like. >>> Please upload your pdb or an image somewhere. >>> >>> Alex >>> >>> On Wed, Jun 27, 2018 at 3:47 AM, Candy Deck >>> wrote: >>> >>> Dear Gromacs Users. I started using Gromacs few month ago. Obviously, I need your help. My system is composed of 2 carbon nanotubes confined between 2 graphene sheets. Closed to each graphene is a box of ionic liquids. My graphene sheets are just here in order to prevent the Ionic liquid to flow around the carbon nanotube. I did minimise my system. The person I'm taking over used to "freeze" the graphene and the CNT. In my case, I use position restrain to the carbon forming the graphene >>> and >>> I restrain the position of the carbon forming the CNT to a plan. I did read that position restrain must be used carrefully as well. I'm realising that this systems is quite complex ... I'm tending to use a compressibility rather low (1.6e-8 bar-1) because I read that the compressibility of Ionic liquid is much more lower than the one of water. after a 500 ps simulation in order to fill the CNTs, there is like a >>> vacuum >>> bubble above the pore. Does someone know what is happening ?? Thanks in advance ! Candy here is my .mpd file : ; RUN CONTROL PARAMETERS = integrator = md ; start time and timestep in ps = tinit= 0 dt = 0.0005 nsteps = 100 ; number of steps for center of mass motion removal = nstcomm = 100 ; LANGEVIN DYNAMICS OPTIONS = ; Temperature, friction coefficient (amu/ps) and random seed = ; bd-temp = 400 ; bd-fric = 0 ; ld-seed = 1993 ; ENERGY MINIMIZATION OPTIONS = ; Force tolerance and initial step-size = emtol= 10 emstep = 0.01 ; Max number of iterations in relax_shells = niter= 20 ; Frequency of steepest descents steps when doing CG = nstcgsteep = 1000 ; OUTPUT CONTROL OPTIONS = ; Output frequency for coords (x), velocities (v) and forces (f) = nstxout = 500 nstvout = 0 nstfout = 500 ; Output frequency for energies to log file and energy file = nstlog = 500 nstenergy= 500 ; Output frequency and precision for xtc file = nstxtcout= 500 xtc-precision= 1000 ; NEIGHBORSEARCHING PARAMETERS = cutoff-scheme= verlet verlet-buffer-tolerance = 0.005 nstlist = 20 ; ns algorithm (simple or grid) = ns_type = grid ; Periodic boundary conditions: xyz or none = pbc = xyz periodic_molecules = yes rlist= 1.0 nstcalclr= 10 ; OPTIONS FOR ELECTROSTATICS AND VDW = ; Method for doing electrostatics = coulombtype = PME coulomb-modifier = Potential-shift rcoulomb-switch = 0 rcoulomb = 0.95 ; Dielectric constant (DC) for cut-off or DC of reaction field = epsilon-r= 1 ; Method for doing Van der Waals = vdw-type = PME vdw-modifier = Potential-shift ; cut-off lengths= rvdw-switch = 0 rvdw = 0.95 ; Apply long range dispersion corrections for Energy and Pressure = DispCorr = No ; Spacing for the PME/PPPM FFT grid = ;fourierspacing = 0.12 ; FFT grid size, when a value is 0
[gmx-users] Potential energy reported by gmx energy command
Hello experts, I did a LJ particles simulation, where I simulated two systems, 100 particle and 400 particle. For 100 particles energy is: Energy Average Err.Est. RMSD Tot-Drift --- Potential 0.126288 0.029 0.615731 -0.0324041 (kJ/mol) Kinetic En. 337.039 0.24 27.6568 0.443176 (kJ/mol) Total Energy 337.165 0.22 27.6615 0.410771 (kJ/mol) For 400 particle energy is: Energy Average Err.Est. RMSD Tot-Drift --- Potential 0.502517 0.042 1.34584 0.220501 (kJ/mol) Kinetic En. 1359 0.82 56.1468 -1.24836 (kJ/mol) Total Energy 1359.5 0.78 56.1548 -1.02787 (kJ/mol) Since both systems have exact same operating conditions, only particle number has been changed, the per particle energy should be same, right? Here I see the energies has become 4 times in the second case. Then what is meaning of reporting energies in "KJ/mol" ? There is nothing like my system is not fully equilibrated, I have thoroughly checked, the both systems are well equilibrated. Please help in understanding these energies. Thank you -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Fwd: Ionic liquid and CNTs
Ah, that's a scary looking system. :) Indeed, there are vacuum pockets, because the system has not been brought to correct pressure. All you have to do for your relaxation run is use a semiisotropic barostat (maybe Berendsen, but only for relaxation) with a realistic solvent compressibility in the Z-direction and zero compressibility in the XY-plane. Gromacs allows this rather easily. And run it for something like 5-10 ns, not 0.5 ns. Alex On 6/28/2018 1:30 AM, Candy Deck wrote: Hi Alex, Thanks for your answer ... Here is the pdb file of my system : https://files.fm/u/7crt2yd5 Candy 2018-06-27 22:30 GMT+02:00 Alex : If there is a bubble, all it could mean is that the volume simply too large, which could be expected, given the combination of short simulation and low compressibility. It is also unclear what your system looks like. Please upload your pdb or an image somewhere. Alex On Wed, Jun 27, 2018 at 3:47 AM, Candy Deck wrote: Dear Gromacs Users. I started using Gromacs few month ago. Obviously, I need your help. My system is composed of 2 carbon nanotubes confined between 2 graphene sheets. Closed to each graphene is a box of ionic liquids. My graphene sheets are just here in order to prevent the Ionic liquid to flow around the carbon nanotube. I did minimise my system. The person I'm taking over used to "freeze" the graphene and the CNT. In my case, I use position restrain to the carbon forming the graphene and I restrain the position of the carbon forming the CNT to a plan. I did read that position restrain must be used carrefully as well. I'm realising that this systems is quite complex ... I'm tending to use a compressibility rather low (1.6e-8 bar-1) because I read that the compressibility of Ionic liquid is much more lower than the one of water. after a 500 ps simulation in order to fill the CNTs, there is like a vacuum bubble above the pore. Does someone know what is happening ?? Thanks in advance ! Candy here is my .mpd file : ; RUN CONTROL PARAMETERS = integrator = md ; start time and timestep in ps = tinit= 0 dt = 0.0005 nsteps = 100 ; number of steps for center of mass motion removal = nstcomm = 100 ; LANGEVIN DYNAMICS OPTIONS = ; Temperature, friction coefficient (amu/ps) and random seed = ; bd-temp = 400 ; bd-fric = 0 ; ld-seed = 1993 ; ENERGY MINIMIZATION OPTIONS = ; Force tolerance and initial step-size = emtol= 10 emstep = 0.01 ; Max number of iterations in relax_shells = niter= 20 ; Frequency of steepest descents steps when doing CG = nstcgsteep = 1000 ; OUTPUT CONTROL OPTIONS = ; Output frequency for coords (x), velocities (v) and forces (f) = nstxout = 500 nstvout = 0 nstfout = 500 ; Output frequency for energies to log file and energy file = nstlog = 500 nstenergy= 500 ; Output frequency and precision for xtc file = nstxtcout= 500 xtc-precision= 1000 ; NEIGHBORSEARCHING PARAMETERS = cutoff-scheme= verlet verlet-buffer-tolerance = 0.005 nstlist = 20 ; ns algorithm (simple or grid) = ns_type = grid ; Periodic boundary conditions: xyz or none = pbc = xyz periodic_molecules = yes rlist= 1.0 nstcalclr= 10 ; OPTIONS FOR ELECTROSTATICS AND VDW = ; Method for doing electrostatics = coulombtype = PME coulomb-modifier = Potential-shift rcoulomb-switch = 0 rcoulomb = 0.95 ; Dielectric constant (DC) for cut-off or DC of reaction field = epsilon-r= 1 ; Method for doing Van der Waals = vdw-type = PME vdw-modifier = Potential-shift ; cut-off lengths= rvdw-switch = 0 rvdw = 0.95 ; Apply long range dispersion corrections for Energy and Pressure = DispCorr = No ; Spacing for the PME/PPPM FFT grid = ;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 ; OPTIONS FOR WEAK COUPLING ALGORITHMS = ; Temperature coupling = tcoupl = V-rescale nsttcouple = 10 ; Groups to couple separately = tc-grps = system ;Time constant (ps) and reference temperature (K) = tau_t= 0.1 ref_t= 293.15 ; Pressure coupling = ;Pcoupl = no Pcoupl = Berendsen Pcoupltype = semiisotropic ; Time
Re: [gmx-users] Fwd: Ionic liquid and CNTs
Hi Alex, Thanks for your answer ... Here is the pdb file of my system : https://files.fm/u/7crt2yd5 Candy 2018-06-27 22:30 GMT+02:00 Alex : > If there is a bubble, all it could mean is that the volume simply too > large, which could be expected, given the combination of short simulation > and low compressibility. It is also unclear what your system looks like. > Please upload your pdb or an image somewhere. > > Alex > > On Wed, Jun 27, 2018 at 3:47 AM, Candy Deck > wrote: > > > Dear Gromacs Users. > > I started using Gromacs few month ago. > > Obviously, I need your help. > > My system is composed of 2 carbon nanotubes confined between 2 graphene > > sheets. > > Closed to each graphene is a box of ionic liquids. > > > > My graphene sheets are just here in order to prevent the Ionic liquid to > > flow around the carbon nanotube. > > > > I did minimise my system. > > The person I'm taking over used to "freeze" the graphene and the CNT. > > In my case, I use position restrain to the carbon forming the graphene > and > > I restrain the position of the carbon forming the CNT to a plan. > > > > I did read that position restrain must be used carrefully as well. > > > > I'm realising that this systems is quite complex ... > > I'm tending to use a compressibility rather low (1.6e-8 bar-1) because I > > read that the compressibility of Ionic liquid is much more lower than the > > one of water. > > after a 500 ps simulation in order to fill the CNTs, there is like a > vacuum > > bubble above the pore. > > > > Does someone know what is happening ?? > > > > Thanks in advance ! > > Candy > > > > here is my .mpd file : > > > > > > ; RUN CONTROL PARAMETERS = > > integrator = md > > ; start time and timestep in ps = > > tinit= 0 > > dt = 0.0005 > > nsteps = 100 > > ; number of steps for center of mass motion removal = > > nstcomm = 100 > > > > ; LANGEVIN DYNAMICS OPTIONS = > > ; Temperature, friction coefficient (amu/ps) and random seed = > > ; bd-temp = 400 > > ; bd-fric = 0 > > ; ld-seed = 1993 > > > > ; ENERGY MINIMIZATION OPTIONS = > > ; Force tolerance and initial step-size = > > emtol= 10 > > emstep = 0.01 > > ; Max number of iterations in relax_shells = > > niter= 20 > > ; Frequency of steepest descents steps when doing CG = > > nstcgsteep = 1000 > > > > ; OUTPUT CONTROL OPTIONS = > > ; Output frequency for coords (x), velocities (v) and forces (f) = > > nstxout = 500 > > nstvout = 0 > > nstfout = 500 > > ; Output frequency for energies to log file and energy file = > > nstlog = 500 > > nstenergy= 500 > > ; Output frequency and precision for xtc file = > > nstxtcout= 500 > > xtc-precision= 1000 > > > > > > ; NEIGHBORSEARCHING PARAMETERS = > > cutoff-scheme= verlet > > verlet-buffer-tolerance = 0.005 > > nstlist = 20 > > ; ns algorithm (simple or grid) = > > ns_type = grid > > ; Periodic boundary conditions: xyz or none = > > pbc = xyz > > > > periodic_molecules = yes > > rlist= 1.0 > > nstcalclr= 10 > > > > ; OPTIONS FOR ELECTROSTATICS AND VDW = > > ; Method for doing electrostatics = > > coulombtype = PME > > coulomb-modifier = Potential-shift > > rcoulomb-switch = 0 > > rcoulomb = 0.95 > > ; Dielectric constant (DC) for cut-off or DC of reaction field = > > epsilon-r= 1 > > ; Method for doing Van der Waals = > > vdw-type = PME > > vdw-modifier = Potential-shift > > ; cut-off lengths= > > rvdw-switch = 0 > > rvdw = 0.95 > > ; Apply long range dispersion corrections for Energy and Pressure = > > DispCorr = No > > ; Spacing for the PME/PPPM FFT grid = > > ;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 > > > > ; OPTIONS FOR WEAK COUPLING ALGORITHMS = > > ; Temperature coupling = > > tcoupl = V-rescale > > nsttcouple = 10 > > ; Groups to couple separately = > > tc-grps = system > > ;Time constant (ps) and reference temperature (K) = > > tau_t= 0.1 > > ref_t= 293.15 > > ; Pressure coupling = > > ;Pcoupl = no > > Pcoupl = Berendsen > > Pcoupltype = semiisotropic > > ; Time
