Re: [gmx-users] DNA-protein complex
The force field that I used was ambe99bsc0, and my input file was: ; 7.3.3 Run Control integrator = md; md integrator tinit = 0 ; [ps] starting time for run dt = 0.002 ; [ps] time step for integration nsteps = 500 ; maximum number of steps to integrate, 0.002 * 2,500,000 = 5,000 ps comm_mode = Linear; remove center of mass translation nstcomm = 1 ; [steps] frequency of mass motion removal comm_grps = Protein Non-Protein ; group(s) for center of mass motion removal ; 7.3.8 Output Control nstxout = 250 ; [steps] freq to write coordinates to trajectory nstvout = 250 ; [steps] freq to write velocities to trajectory nstfout = 250 ; [steps] freq to write forces to trajectory nstlog = 100 ; [steps] freq to write energies to log file nstenergy = 500 ; [steps] freq to write energies to energy file nstxtcout = 500 ; [steps] freq to write coordinates to xtc trajectory xtc_precision = 1000 ; [real] precision to write xtc trajectory xtc_grps= System; group(s) to write to xtc trajectory energygrps = System; group(s) to write to energy file ; 7.3.9 Neighbor Searching nstlist = 1 ; [steps] freq to update neighbor list ns_type = grid ; method of updating neighbor list pbc = xyz ; periodic boundary conditions in all directions rlist = 0.8 ; [nm] cut-off distance for the short-range neighbor list ; 7.3.10 Electrostatics coulombtype = PME ; Particle-Mesh Ewald electrostatics rcoulomb= 0.8 ; [nm] distance for Coulomb cut-off ; 7.3.11 VdW vdwtype = cut-off ; twin-range cut-off with rlist where rvdw = rlist rvdw= 0.8 ; [nm] distance for LJ cut-off DispCorr= EnerPres ; apply long range dispersion corrections for energy ; 7.3.13 Ewald fourierspacing = 0.12 ; [nm] grid spacing for FFT grid when using PME pme_order = 4 ; interpolation order for PME, 4 = cubic ewald_rtol = 1e-5 ; relative strength of Ewald-shifted potential at rcoulomb ; 7.3.14 Temperature Coupling tcoupl = v-rescale ; temperature coupling with Nose-Hoover ensemble tc_grps = ProteinNon-Protein; groups to couple seperately to temperature bath tau_t = 0.10.1; [ps] time constant for coupling ref_t = 310310; [K] reference temperature for coupling ; 7.3.15 Pressure Coupling pcoupl = parrinello-rahman ; pressure coupling where box vectors are variable pcoupltype = isotropic ; pressure coupling in x-y-z directions tau_p = 2.0 ; [ps] time constant for coupling compressibility = 4.5e-5; [bar^-1] compressibility ref_p = 1.0 ; [bar] reference pressure for coupling ; 7.3.17 Velocity Generation gen_vel = no; velocity generation turned off ; 7.3.18 Bonds constraints = all-bonds ; convert all bonds to constraints constraint_algorithm= LINCS ; LINear Constraint Solver continuation= yes ; apply constraints to the start configuration lincs_order = 4 ; highest order in the expansion of the contraint coupling matrix lincs_iter = 1 ; number of iterations to correct for rotational lengthening lincs_warnangle = 30; [degrees] maximum angle that a bond can rotate before LINCS will complain best regards Urszula Uciechowska 2015-03-17 14:35 GMT-03:00 Urszula Uciechowska urszula.uciechow...@biotech.ug.edu.pl: Hi, I am running MD for dsDNA-protein complex. After 50ns I observed that the DNA is unwinding. What did go wrong? Should I have changed something in my input file? You might want to send your input files, so as your force field that you have choose. It is hard to say anything without more details. Also, what do you mean by 'unwinding'? Could you be more specific? Thank you in advance for your suggestions. best regards Urszula Cheers! -- Marcelo Depólo Polêto B.Sc. Biochemistry - University of Viçosa (Brazil) -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read
[gmx-users] comparison of entropy and enthalpy at different temperatures
Hi, I'll be happy if some one can help. I have a large system containing of 17000 water molecules and 1000 lutidine molecules. I am simulating the mixture at different temperatures, T, close to the mixture's critical point. I want to investigate competition between entropy and enthalpy at different T. What is the easiest and fast way? I think of following ideas, 1- Just take a single lutidine and obtain free energy of salvation (from pure water) at different temperatures, T, moreover I have enthalpy from g_energy, so I can obtain entropy for each T. 2- obtaining entropy by g_cover and g_anaeig, and enthalpy from g_energy at each T. but this is hard because the system is very big. I tested and failed. are they good ways? Best regards -- 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] A jump in potential just after extension
Dear Justin, I use gromacs/4.6.7. http://4.6.0.7/ Below is my .mdp file. No that is not similar to my case, I do not change any setting for the extension. (I should add that despite strange jump in potential in g_energy, the trajectory goes in a direction which I expect.) PRODUCTIOn integrator= md dt= 0.002 nsteps= 5000 nstxout = 1 ; save coordinates every ps nstvout = 1 ; save velocities every ps nstlog = 1 ; update log file every nstenergy = 1 ; save energies every nstxtcout= 10 ; Output frequency for xtc file xtc-precision = 10 ; precision for xtc file ns_type= grid; search neighboring grid cells nstlist= 5; fs pbc= xyz ; 3-D PBC rlist= 1.2 ; short-range neighborlist cutoff (in nm) rcoulomb= 1.2 ; short-range electrostatic cutoff (in nm) rvdw = 1.2 ; short-range van der Waals cutoff (in nm) coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics pme_order = 4 ; cubic interpolation fourierspacing= 0.16; grid spacing for FFT vdw-type= Cut-off Tcoupl= v-rescale ; modified Berendsen thermostat tc-grps = LUT SOL ; two coupling groups - more accurate tau_t = 0.1 0.1 ; time constant, in ps ref_t= 380. 380. ; reference temperature, one for each group, in K ;tc-grps = system energygrps = LUT SOL Pcoupl= Parrinello-Rahman Pcoupltype = Isotropic tau_p = 1.0 compressibility = 4.5e-5 ref_p= 1.0 gen_vel= no gen_temp= 380.0 gen_seed= 712349 DispCorr = EnerPres; account for cut-off vdW scheme constraints = all-bonds ; all bonds constrained (fixed length) continuation = yes ; Restarting after NPT constraint-algorithm = lincs ; holonomic constraints lincs_iter= 1 ; accuracy of LINCS lincs_order= 4 ; also related to accuracy ** Best regards Dear Justin, I use gromacs/4.6.7. Below is my .mdp file. No that is not similar to my case, I do not change any setting for the extension. (I should add that despite strange jump in potential in g_energy, the trajectory goes in a direction which I expect.) PRODUCTIOn integrator= md dt= 0.002 nsteps= 5000 nstxout = 1 ; save coordinates every ps nstvout = 1 ; save velocities every ps nstlog = 1 ; update log file every nstenergy = 1 ; save energies every nstxtcout= 10 ; Output frequency for xtc file xtc-precision = 10 ; precision for xtc file ns_type = grid; search neighboring grid cells nstlist = 5; fs pbc = xyz ; 3-D PBC rlist = 1.2 ; short-range neighborlist cutoff (in nm) rcoulomb = 1.2 ; short-range electrostatic cutoff (in nm) rvdw = 1.2 ; short-range van der Waals cutoff (in nm) coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics pme_order = 4 ; cubic interpolation fourierspacing= 0.16; grid spacing for FFT vdw-type= Cut-off Tcoupl= v-rescale ; modified Berendsen thermostat tc-grps = LUT SOL ; two coupling groups - more accurate tau_t = 0.1 0.1 ; time constant, in ps ref_t= 380. 380. ; reference temperature, one for each group, in K ;tc-grps = system energygrps = LUT SOL Pcoupl= Parrinello-Rahman Pcoupltype = Isotropic tau_p = 1.0 compressibility = 4.5e-5 ref_p= 1.0 gen_vel= no gen_temp= 380.0 gen_seed
Re: [gmx-users] DNA-protein complex
2015-03-18 5:26 GMT-03:00 Urszula Uciechowska urszula.uciechow...@biotech.ug.edu.pl: The force field that I used was ambe99bsc0, and my input file was: ; 7.3.3 Run Control integrator = md; md integrator tinit = 0 ; [ps] starting time for run dt = 0.002 ; [ps] time step for integration nsteps = 500 ; maximum number of steps to integrate, 0.002 * 2,500,000 = 5,000 ps comm_mode = Linear; remove center of mass translation nstcomm = 1 ; [steps] frequency of mass motion removal comm_grps = Protein Non-Protein ; group(s) for center of mass motion removal ; 7.3.8 Output Control nstxout = 250 ; [steps] freq to write coordinates to trajectory nstvout = 250 ; [steps] freq to write velocities to trajectory nstfout = 250 ; [steps] freq to write forces to Why such a low output frequency? You are writing every 5ns.. this is too high for any kind of small system simulation. trajectory nstlog = 100 ; [steps] freq to write energies to log file nstenergy = 500 ; [steps] freq to write energies to energy file nstxtcout = 500 ; [steps] freq to write coordinates to xtc trajectory xtc_precision = 1000 ; [real] precision to write xtc trajectory xtc_grps= System; group(s) to write to xtc trajectory energygrps = System; group(s) to write to energy file ; 7.3.9 Neighbor Searching nstlist = 1 ; [steps] freq to update neighbor list ns_type = grid ; method of updating neighbor list pbc = xyz ; periodic boundary conditions in all directions rlist = 0.8 ; [nm] cut-off distance for the short-range neighbor list ; 7.3.10 Electrostatics coulombtype = PME ; Particle-Mesh Ewald electrostatics rcoulomb= 0.8 ; [nm] distance for Coulomb cut-off ; 7.3.11 VdW vdwtype = cut-off ; twin-range cut-off with rlist where rvdw = rlist rvdw= 0.8 ; [nm] distance for LJ cut-off DispCorr= EnerPres ; apply long range dispersion corrections for energy ; 7.3.13 Ewald fourierspacing = 0.12 ; [nm] grid spacing for FFT grid when using PME pme_order = 4 ; interpolation order for PME, 4 = cubic ewald_rtol = 1e-5 ; relative strength of Ewald-shifted potential at rcoulomb ; 7.3.14 Temperature Coupling tcoupl = v-rescale ; temperature coupling with Nose-Hoover ensemble tc_grps = ProteinNon-Protein; groups to couple seperately to temperature bath tau_t = 0.10.1; [ps] time constant for coupling ref_t = 310310; [K] reference temperature for coupling ; 7.3.15 Pressure Coupling pcoupl = parrinello-rahman ; pressure coupling where box vectors are variable pcoupltype = isotropic ; pressure coupling in x-y-z directions tau_p = 2.0 ; [ps] time constant for coupling compressibility = 4.5e-5; [bar^-1] compressibility ref_p = 1.0 ; [bar] reference pressure for coupling ; 7.3.17 Velocity Generation gen_vel = no; velocity generation turned off ; 7.3.18 Bonds constraints = all-bonds ; convert all bonds to constraints constraint_algorithm= LINCS ; LINear Constraint Solver continuation= yes ; apply constraints to the start configuration lincs_order = 4 ; highest order in the expansion of the contraint coupling matrix lincs_iter = 1 ; number of iterations to correct for rotational lengthening lincs_warnangle = 30; [degrees] maximum angle that a bond can rotate before LINCS will complain It remains difficult to foresee anything without the protocol that you have used. Just the production mdp file will not provide enough info to say anything. Please send your protocol and mdp files. Cheers! -- Marcelo Depólo Polêto Student of MSc Cell and Molecular Biology - UFRGS (Brazil) B.Sc. Biochemistry - University of Viçosa (Brazil) -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists *
Re: [gmx-users] jump problem
On 3/17/15 9:03 PM, Ahmet yıldırım wrote: Dear users, I tried to remove the jumps of a structure after simulation but I couldn't do it. The structure is heterodimer. I tried the following ways: 1) -gmx trjconv -f md.xtc -s md.tpr -o traj_nojump.xtc -pbc nojump -gmx trjconv -f traj_nojump.xtc -s md.tpr -o traj_center.xtc -pbc mol -ur compact -center 2) gmx trjconv -f md.xtc -s md.tpr -o traj_nojump.xtc -pbc nojump -center 3) -gmx trjconv -f md.xtc -s md.tpr -o traj_nojump.xtc -pbc nojump -center -gmx trjconv -f traj_nojump.xtc -s md.tpr -o traj_center.xtc -fit rot+trans Do you have any suggestion(s)? Fitting to any default group is unlikely to work in multimeric systems. Use a custom index group to center on one subunit or some selected subset of atoms in one protein (e.g. some interfacial residues, or something convenient). -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] jump problem
Hey :) Cluster the first frame and write out as new reference structure. Then run with that reference, removing jumps. Cheers, Tsjerk On Mar 18, 2015 12:46 PM, Justin Lemkul jalem...@vt.edu wrote: On 3/17/15 9:03 PM, Ahmet yıldırım wrote: Dear users, I tried to remove the jumps of a structure after simulation but I couldn't do it. The structure is heterodimer. I tried the following ways: 1) -gmx trjconv -f md.xtc -s md.tpr -o traj_nojump.xtc -pbc nojump -gmx trjconv -f traj_nojump.xtc -s md.tpr -o traj_center.xtc -pbc mol -ur compact -center 2) gmx trjconv -f md.xtc -s md.tpr -o traj_nojump.xtc -pbc nojump -center 3) -gmx trjconv -f md.xtc -s md.tpr -o traj_nojump.xtc -pbc nojump -center -gmx trjconv -f traj_nojump.xtc -s md.tpr -o traj_center.xtc -fit rot+trans Do you have any suggestion(s)? Fitting to any default group is unlikely to work in multimeric systems. Use a custom index group to center on one subunit or some selected subset of atoms in one protein (e.g. some interfacial residues, or something convenient). -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/ Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] DNA-protein complex
On 3/18/15 4:26 AM, Urszula Uciechowska wrote: The force field that I used was ambe99bsc0, and my input file was: What is the DNA sequence? We have seen some cases where AMBER99-parmbsc0 fails to capture global characteristics of DNA structure. This is a common problem among additive nucleic acid force fields. In general, AMBER and CHARMM parameter sets are quite good, but there are times when they can fail. See, for instance, a comparison including this AMBER parameter set in http://dx.doi.org/10.1021/jz5024543 -Justin ; 7.3.3 Run Control integrator = md; md integrator tinit = 0 ; [ps] starting time for run dt = 0.002 ; [ps] time step for integration nsteps = 500 ; maximum number of steps to integrate, 0.002 * 2,500,000 = 5,000 ps comm_mode = Linear; remove center of mass translation nstcomm = 1 ; [steps] frequency of mass motion removal comm_grps = Protein Non-Protein ; group(s) for center of mass motion removal ; 7.3.8 Output Control nstxout = 250 ; [steps] freq to write coordinates to trajectory nstvout = 250 ; [steps] freq to write velocities to trajectory nstfout = 250 ; [steps] freq to write forces to trajectory nstlog = 100 ; [steps] freq to write energies to log file nstenergy = 500 ; [steps] freq to write energies to energy file nstxtcout = 500 ; [steps] freq to write coordinates to xtc trajectory xtc_precision = 1000 ; [real] precision to write xtc trajectory xtc_grps= System; group(s) to write to xtc trajectory energygrps = System; group(s) to write to energy file ; 7.3.9 Neighbor Searching nstlist = 1 ; [steps] freq to update neighbor list ns_type = grid ; method of updating neighbor list pbc = xyz ; periodic boundary conditions in all directions rlist = 0.8 ; [nm] cut-off distance for the short-range neighbor list ; 7.3.10 Electrostatics coulombtype = PME ; Particle-Mesh Ewald electrostatics rcoulomb= 0.8 ; [nm] distance for Coulomb cut-off ; 7.3.11 VdW vdwtype = cut-off ; twin-range cut-off with rlist where rvdw = rlist rvdw= 0.8 ; [nm] distance for LJ cut-off DispCorr= EnerPres ; apply long range dispersion corrections for energy ; 7.3.13 Ewald fourierspacing = 0.12 ; [nm] grid spacing for FFT grid when using PME pme_order = 4 ; interpolation order for PME, 4 = cubic ewald_rtol = 1e-5 ; relative strength of Ewald-shifted potential at rcoulomb ; 7.3.14 Temperature Coupling tcoupl = v-rescale ; temperature coupling with Nose-Hoover ensemble tc_grps = ProteinNon-Protein; groups to couple seperately to temperature bath tau_t = 0.10.1; [ps] time constant for coupling ref_t = 310310; [K] reference temperature for coupling ; 7.3.15 Pressure Coupling pcoupl = parrinello-rahman ; pressure coupling where box vectors are variable pcoupltype = isotropic ; pressure coupling in x-y-z directions tau_p = 2.0 ; [ps] time constant for coupling compressibility = 4.5e-5; [bar^-1] compressibility ref_p = 1.0 ; [bar] reference pressure for coupling ; 7.3.17 Velocity Generation gen_vel = no; velocity generation turned off ; 7.3.18 Bonds constraints = all-bonds ; convert all bonds to constraints constraint_algorithm= LINCS ; LINear Constraint Solver continuation= yes ; apply constraints to the start configuration lincs_order = 4 ; highest order in the expansion of the contraint coupling matrix lincs_iter = 1 ; number of iterations to correct for rotational lengthening lincs_warnangle = 30; [degrees] maximum angle that a bond can rotate before LINCS will complain best regards Urszula Uciechowska 2015-03-17 14:35 GMT-03:00 Urszula Uciechowska urszula.uciechow...@biotech.ug.edu.pl: Hi, I am running MD for dsDNA-protein complex. After 50ns I observed that the DNA is unwinding. What did go wrong? Should I have changed something in my input file? You might want to send your input files, so as your force field that you have
Re: [gmx-users] umbrella sampling tutorial
On 3/17/15 9:06 PM, Ming Tang wrote: Hi Justin, Thanks a lot. I can move forward now. Recently, I am trying to pull a triple helix, and want to fix the center of mass of the three terminal atoms. One paper said that it can be done by means of a strong harmonic restrain with a super large spring constant in Gromos96 53 a6. But I still don't know how to do this. Can you give me some advice? Absolute restraints can be used in the pull code, but I've never done it. Note that such an approach is incompatible with NPT. Freezing may also be an option, but then you're acting directly on all the atoms and frozen groups carry their own artificiality. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] PDB for nafion
Dear all, I want to simulate nafion oligomers in explicit water. Is there any tool or any software where I can build a short nafion residue? How consistent will be the bond length/angle parameters with respect to the employed force field? I am quite new in the filed of molecular dynamics and hope I am not asking for much...:) Regards, Soumadwip Ghosh Research Fellow, IIT Bombay, India -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] error while equilibration
I am trying to simulate RNA in water. I have minimized the system with steepest Decent for 2000 steps and then with Conjugate gradient for till the energy coverage reaches to 100 Kj/mol. But when I am trying to equilibrate it I am getting following error --- Program mdrun, VERSION 4.5.5 Source code file: /build/buildd/gromacs-4.5.5/src/mdlib/pme.c, line: 538 Fatal error: 11 particles communicated to PME node 3 are more than 2/3 times the cut-off out of the domain decomposition cell of their charge group in dimension x. This usually means that your system is not well equilibrated. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- My nvt.mdp file contain title = RNA complex NVT equilibration define = -DPOSRES ; position restrain ; Run parameters integrator = md; leap-frog integrator nsteps = 5 ; 2 * 5 = 100 ps dt = 0.002 ; 2 fs ; Output control nstxout = 100 ; save coordinates every 0.2 ps nstvout = 100 ; save velocities every 0.2 ps nstenergy = 100 ; save energies every 0.2 ps nstlog = 100 ; update log file every 0.2 ps energygrps = RNA SOL NA ; Bond parameters continuation= no; first dynamics run constraint_algorithm = lincs; holonomic constraints constraints = all-bonds ; all bonds (even heavy atom-H bonds) constrained lincs_iter = 1 ; accuracy of LINCS lincs_order = 4 ; also related to accuracy ; Neighborsearching ns_type = grid ; search neighboring grid cells nstlist = 5 ; 10 fs rlist = 0.9 ; short-range neighborlist cutoff (in nm) rcoulomb= 0.9 ; short-range electrostatic cutoff (in nm) rvdw= 1.4 ; short-range van der Waals cutoff (in nm) ; Electrostatics coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics pme_order = 4 ; cubic interpolation fourierspacing = 0.16 ; grid spacing for FFT ; Temperature coupling tcoupl = V-rescale ; modified Berendsen thermostat tc-grps = RNA SOL NA ; two coupling groups - more accurate tau_t = 0.1 0.1 0.1 ; time constant, in ps ref_t = 310 310 310; reference temperature, one for each group, in K ; Pressure coupling pcoupl = no; no pressure coupling in NVT ; Periodic boundary conditions pbc = xyz ; 3-D PBC ; Dispersion correction DispCorr= EnerPres ; account for cut-off vdW scheme ; Velocity generation gen_vel = yes ; assign velocities from Maxwell distribution gen_temp= 310 ; temperature for Maxwell distribution gen_seed= -1; generate a random seed Please tell me where I am doing wrong. -- Ananya Chatterjee, Senior Research Fellow (SRF), Department of biological Science, IISER-Kolkata. -- 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] error while equilibration
On 3/18/15 12:01 PM, ananyachatterjee wrote: I am trying to simulate RNA in water. I have minimized the system with steepest Decent for 2000 steps and then with Conjugate gradient for till the energy coverage reaches to 100 Kj/mol. But when I am trying to equilibrate it I am getting following error What's the actual output in terms of Epot and Fmax? What force field are you using? --- Program mdrun, VERSION 4.5.5 Source code file: /build/buildd/gromacs-4.5.5/src/mdlib/pme.c, line: 538 Fatal error: 11 particles communicated to PME node 3 are more than 2/3 times the cut-off out of the domain decomposition cell of their charge group in dimension x. This usually means that your system is not well equilibrated. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- My nvt.mdp file contain title = RNA complex NVT equilibration define = -DPOSRES ; position restrain ; Run parameters integrator = md; leap-frog integrator nsteps = 5 ; 2 * 5 = 100 ps dt = 0.002 ; 2 fs ; Output control nstxout = 100 ; save coordinates every 0.2 ps nstvout = 100 ; save velocities every 0.2 ps nstenergy = 100 ; save energies every 0.2 ps nstlog = 100 ; update log file every 0.2 ps energygrps = RNA SOL NA ; Bond parameters continuation= no; first dynamics run constraint_algorithm = lincs; holonomic constraints constraints = all-bonds ; all bonds (even heavy atom-H bonds) constrained lincs_iter = 1 ; accuracy of LINCS lincs_order = 4 ; also related to accuracy ; Neighborsearching ns_type = grid ; search neighboring grid cells nstlist = 5 ; 10 fs rlist = 0.9 ; short-range neighborlist cutoff (in nm) rcoulomb= 0.9 ; short-range electrostatic cutoff (in nm) rvdw= 1.4 ; short-range van der Waals cutoff (in nm) I doubt these settings are right for any of the reliable nucleic acid force fields I know of, but you'll have to answer the question above. ; Electrostatics coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics pme_order = 4 ; cubic interpolation fourierspacing = 0.16 ; grid spacing for FFT ; Temperature coupling tcoupl = V-rescale ; modified Berendsen thermostat tc-grps = RNA SOL NA ; two coupling groups - more accurate Don't couple solvent and ions separately. http://www.gromacs.org/Documentation/Terminology/Thermostats#What_Not_To_Do -Justin tau_t = 0.1 0.1 0.1 ; time constant, in ps ref_t = 310 310 310; reference temperature, one for each group, in K ; Pressure coupling pcoupl = no; no pressure coupling in NVT ; Periodic boundary conditions pbc = xyz ; 3-D PBC ; Dispersion correction DispCorr= EnerPres ; account for cut-off vdW scheme ; Velocity generation gen_vel = yes ; assign velocities from Maxwell distribution gen_temp= 310 ; temperature for Maxwell distribution gen_seed= -1; generate a random seed Please tell me where I am doing wrong. -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Error while shrinking lipids (KALP15 in DPPC tutorial)
On 3/18/15 4:05 PM, Thomas Lipscomb wrote: Dear gmx-users, This means someone has removed gb.itp from the charmm36.ff directory and hence grompp fails. If someone has been toying with the contents of the force field, start fresh with a new tarball from: http://mackerell.umaryland.edu/charmm_ff.shtml#gromacs. -Justin Thanks. Strangely, charmm36.ff already had gb.itp, but what fixed that file not found error that was copying all of the files (including gb.itp) from: /usr/local/gromacs/share/gromacs/top/charmm36.ff to my working directory: /home/tlipscomb/Desktop/Antimicrobial_Peptides/Gromacs/KALP/charmm36_lipid.ff While not overwriting the modified files that were already in charmm36_lipid.ff I have no idea why this works. But now I am getting the error: ---Program gmx, VERSION 5.0.1Source code file: /home/tlipscomb/gromacs-5.0.1/src/gromacs/gmxpreprocess/grompp.c, line: 603 Fatal error:number of coordinates in coordinate file (system_shrink1.gro, 6400) does not match topology (topol.top, 6802)For more information and tips for troubleshooting, please check the GROMACSwebsite at http://www.gromacs.org/Documentation/Errors--- topol.top has this: [ molecules ]; Compound#molsProtein_chain_A 1DPPC 128 But the system_shrink1.gro only has the DPPC not the protein. The protein has 402 coordinates so clearly system_shrink1.gro not having the 402 protein coordinates is the problem. Do I copy the 402 protein coordinates from [ atoms ] in topol.top to system_shrink1.gro? The coordinates seem to be in different formats. Topologies are not coordinates. You need to actually construct the system correctly. If you have only DPPC, then you don't have a protein, which means you've probably forgotten to do something. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] potential energy is from energy mimization
Dear gmx, I am simulation a kinase protein which has (~1200 aa) length. When I energy minimize the protein with default em file from Justin A. Lemku tutorial. i have got the following output. writing lowest energy coordinates. Steepest Descents converged to Fmax 1000 in 1162 steps Potential Energy = -4.6686910e+06 Maximum force = 9.6213324e+02 on atom 10673 Norm of force = 1.6875889e+01 After i plot the potential and through gmx energy -f em.edr -o potential.xvg by selecting potential (15) and 0, i end up with following results.. Energy Average Err.Est. RMSD Tot-Drift --- Potential1.97914e+09 2e+09 5.83904e+10 -1.18272e+10 (kJ/mol) When i try to see this value in xmgrace plot, i ccouldnt see any plot. Doesnt mean my system is not relaxed well? Should i need to increase the steps of em ? if so, how do i ? Thanks. -- 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] Core Dump
Hi All, I am using GRMACS 5.0.4, I got and error: Core dump on signal SIGBUS (7) suppressed. There was a warning: This run will generate roughly 3298 Mb of data. Kind regards, Alex -- 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] Core Dump
Hi, Thanks for help. It was not grommp fault. The command line was mdrun_mpi -ntomp 1 -s relaxation.tp -deffnm relaxation -c HAP_relaxation.pdb Hope following can help. MPT: On host cl2n109, Program /pkg/suse11/gromacs/5.0.4/bin/gmx_mpi, Rank 0, Process 220661: Dumping core on signal SIGBUS(7) into directory /home/huangb2/test MPT: Program /pkg/suse11/gromacs/5.0.4/bin/gmx_mpi, Rank 1, Process 220662: Core dump on signal SIGBUS(7) suppressed. MPT: Program /pkg/suse11/gromacs/5.0.4/bin/gmx_mpi, Rank 2, Process 220663: Core dump on signal SIGBUS(7) suppressed. MPT: Program /pkg/suse11/gromacs/5.0.4/bin/gmx_mpi, Rank 3, Process 220664: Core dump on signal SIGBUS(7) suppressed. MPT: MPI_COMM_WORLD rank 0 has terminated without calling MPI_Finalize() aborting job MPT: Received signal 7 Kind regards, Alex -Original Message- From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Justin Lemkul Sent: Thursday, 19 March 2015 10:05 AM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Core Dump On 3/18/15 7:48 PM, BAOLIN HUANG wrote: Hi All, I am using GRMACS 5.0.4, I got and error: Core dump on signal SIGBUS (7) suppressed. There was a warning: This run will generate roughly 3298 Mb of data. So grompp seg faults? You're going to have to provide real information, like what your command was, relevant output, etc. There's nothing that can be diagnosed here. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] How to set a system consists of membranes and cholestrols
Dear gmx_users, Hello, I want to simulate membrane system that contains lipids, cholestrols and glycolipids. Is there any suggestions, advice and some useful links? Best regards, Batsaikhan -- 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] Core Dump
On 3/18/15 7:48 PM, BAOLIN HUANG wrote: Hi All, I am using GRMACS 5.0.4, I got and error: Core dump on signal SIGBUS (7) suppressed. There was a warning: This run will generate roughly 3298 Mb of data. So grompp seg faults? You're going to have to provide real information, like what your command was, relevant output, etc. There's nothing that can be diagnosed here. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] changing partial charge/atom type upon covalent bonding
Dear users, I need to simulate a protein which is covalently bonded to some covalent inhibitors using GROMACS 5.0.4 and the AMBER99SB-ILDN force field. Thanks to the user discussion list I successfully used specbond.dat and suitable modifications in a local copy of the forcefield to make the relevant bonds between the protein and the inhibitors. However, I have a specific question about how account for the effect of the new bonds on the pre-existing parameters. As an example, let's take an ester bond with a Glutamate side chain. I added it to specbond.dat. The GLU side chain partial charges and atom types should change as a result of the covalent bond. Hence, I created the GLX residue so I can change its partial charges and atom types. But how should I derive them? My idea is to make a GAFF/Antechamber/acpype parametrization of the ligand bound to a glutamate residue. By doing this, I will be able to get the charges and atomtypes for the bonded residue and add them to the forcefield as the post bond GLX residue. Additionally, I will have better parameters for describing this new bond itself. Is this approach correct? Any suggestions? Thank you for your attention, Leandro. -- 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 is from energy mimization
On 3/18/15 9:42 PM, Rj wrote: Dear gmx, I am simulation a kinase protein which has (~1200 aa) length. When I energy minimize the protein with default em file from Justin A. Lemku tutorial. i have got the following output. writing lowest energy coordinates. Steepest Descents converged to Fmax 1000 in 1162 steps Potential Energy = -4.6686910e+06 Maximum force = 9.6213324e+02 on atom 10673 Norm of force = 1.6875889e+01 After i plot the potential and through gmx energy -f em.edr -o potential.xvg by selecting potential (15) and 0, i end up with following results.. Energy Average Err.Est. RMSD Tot-Drift --- Potential1.97914e+09 2e+09 5.83904e+10 -1.18272e+10 (kJ/mol) The average potential during EM has no use. When i try to see this value in xmgrace plot, i ccouldnt see any plot. Doesnt mean my system is not relaxed well? Should i need to increase the steps of em ? if so, how do i ? Thanks. Probably the potential just drops precipitously and the resulting scale is such that you can't clearly see it. Look at the .xvg in a text editor and you will see the progression of the energy, or adjust the scale in Grace. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Core Dump
On 3/18/15 8:51 PM, BAOLIN HUANG wrote: Hi, Thanks for help. It was not grommp fault. The command line was mdrun_mpi -ntomp 1 -s relaxation.tp -deffnm relaxation -c HAP_relaxation.pdb Hope following can help. MPT: On host cl2n109, Program /pkg/suse11/gromacs/5.0.4/bin/gmx_mpi, Rank 0, Process 220661: Dumping core on signal SIGBUS(7) into directory /home/huangb2/test MPT: Program /pkg/suse11/gromacs/5.0.4/bin/gmx_mpi, Rank 1, Process 220662: Core dump on signal SIGBUS(7) suppressed. MPT: Program /pkg/suse11/gromacs/5.0.4/bin/gmx_mpi, Rank 2, Process 220663: Core dump on signal SIGBUS(7) suppressed. MPT: Program /pkg/suse11/gromacs/5.0.4/bin/gmx_mpi, Rank 3, Process 220664: Core dump on signal SIGBUS(7) suppressed. MPT: MPI_COMM_WORLD rank 0 has terminated without calling MPI_Finalize() aborting job MPT: Received signal 7 Nope, that's just a generic failure. Check the .log file for any specific message from GROMACS. Likely there's some immediate, catastrophic failure. If you're lucky, mdrun will have printed the initial conditions, which can be used to spot the problem. -Justin Kind regards, Alex -Original Message- From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Justin Lemkul Sent: Thursday, 19 March 2015 10:05 AM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Core Dump On 3/18/15 7:48 PM, BAOLIN HUANG wrote: Hi All, I am using GRMACS 5.0.4, I got and error: Core dump on signal SIGBUS (7) suppressed. There was a warning: This run will generate roughly 3298 Mb of data. So grompp seg faults? You're going to have to provide real information, like what your command was, relevant output, etc. There's nothing that can be diagnosed here. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] pdb2gmx error
Dear gmx, I tried to to use pdb2gmx and get this error for 3 to 4 residues. I even cleaned my crystal structure using Discovery studio/swissviewer which shows no error on it. I wonder, how do i rectify this problem ? WARNING: WARNING: Residue 1 named MET of a molecule in the input file was mapped to an entry in the topology database, but the atom H used in an interaction of type angle in that entry is not found in the input file. Perhaps your atom and/or residue naming needs to be fixed. WARNING: WARNING: Residue 366 named LEU of a molecule in the input file was mapped to an entry in the topology database, but the atom O used in an interaction of type angle in that entry is not found in the input file. Perhaps your atom and/or residue naming needs to be fixed. Before cleaning: 7060 pairs Residue 32681 named GLN of a molecule in the input file was mapped to an entry in the topology database, but the atom N used in an interaction of type improper in that entry is not found in the input file. Perhaps your atom and/or residue naming needs to be fixed. -- 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] Membrane simulation
Hi,I want to simulate membrane system that contains lipids, cholesterol and glycolipid. Is it possible to simulate entire membrane structure. Kindle help me to simulate such system.Thank you, With Regards, A.Petrishia Department of ECE, College of Engineering,Guindy, Anna University, Chennai-600025 9444689919 -- 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] g_dist
hello everyone i am unable to understand the result of gmx check .it gives frames and time values .g_dist is worked in all protein related residues but i want to calculate the distance between some residues of protein and ligand for ligand i got same problem like mismatch. kindly help On Mon, Mar 16, 2015 at 5:02 PM, Justin Lemkul jalem...@vt.edu wrote: On 3/16/15 6:43 AM, RINU KHATTRI wrote: hello everyone I am working on protein complex with popc membrane gromcs version is 4.5.5 i want to calculate the distance between two residues during the simulation (200ns) i have been made the .ndx file of atoms of two residues and concatenate .xtc file and final .tpr file g_dist -f full.xtc -s final.tpr -n atom.ndx -o dist.xvg Molecule in topology has atom numbers below and above natoms (3893). You are probably trying to use a trajectory which does not match the first 3893 atoms of the run input file. You can make a matching run input file with tpbconv. the indx file is having the atom no which are present in last.gro file kindly help So what does gmxcheck tell you about the contents of the .tpr and the .xtc? Likely you have a mismatch in what you saved to the trajectory either in the run or when using trjconv at some point. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Tutorial For Installing Gromacs on window
Greetings, I want to install gromacs on window 7. but i don't know the exact procedure.could you please explain me the procedure to install gromacs on window. Thanking you in anticipation -- 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] distribution of water molecules
Dear all, I have a box of water molecules and a peptite amphiphile based cylindirical nanofiber. I would like to find the density distribution of water. To do this: 1) I created an index file which contains OW atoms (=Oxygen atoms that belong to the water molecules) 2) Then, I used the following command: g_rdf -f traj.xtc -s OW.ndx -o rdf.gro To be able to continue one needs to choose a reference group and the other group. How does this work: for example how should I choose these groups? Also, Could the same procedures be used to compute the distribution of sodium ions? Thank you for your help. Turgay -- 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] Error while shrinking lipids (KALP15 in DPPC tutorial)
Dear gmx-users, This means someone has removed gb.itp from the charmm36.ff directory and hence grompp fails. If someone has been toying with the contents of the force field, start fresh with a new tarball from: http://mackerell.umaryland.edu/charmm_ff.shtml#gromacs. -Justin Thanks. Strangely, charmm36.ff already had gb.itp, but what fixed that file not found error that was copying all of the files (including gb.itp) from: /usr/local/gromacs/share/gromacs/top/charmm36.ff to my working directory: /home/tlipscomb/Desktop/Antimicrobial_Peptides/Gromacs/KALP/charmm36_lipid.ff While not overwriting the modified files that were already in charmm36_lipid.ff But now I am getting the error: ---Program gmx, VERSION 5.0.1Source code file: /home/tlipscomb/gromacs-5.0.1/src/gromacs/gmxpreprocess/grompp.c, line: 603 Fatal error:number of coordinates in coordinate file (system_shrink1.gro, 6400) does not match topology (topol.top, 6802)For more information and tips for troubleshooting, please check the GROMACSwebsite at http://www.gromacs.org/Documentation/Errors--- topol.top has this: [ molecules ]; Compound #molsProtein_chain_A 1DPPC 128 But the system_shrink1.gro only has the DPPC not the protein. The protein has 402 coordinates so clearly system_shrink1.gro not having the 402 protein coordinates is the problem. Do I copy the 402 protein coordinates from [ atoms ] in topol.top to system_shrink1.gro? The coordinates seem to be in different formats. Sincerely,Thomas -- 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.
