Re: [gmx-users] Distance restraints exploding system
To wrap this up for anyone who stumbles across this in the future: The 'solution' I ended up going with was to avoid using hydrogen atoms in the restraints, instead restraining to the e.g. methyl carbon and adding a fudge factor to the restraint length to account for the C-H distance. This results in slightly 'looser' restraints but actually runs stably. -Trayder On Tue, Sep 3, 2013 at 5:32 AM, Rafael I. Silverman y de la Vega rsilv...@ucsc.edu wrote: Have you tried with even less restraints? I found systems are not always stable with more than the bare minimum of restraints On Sun, Sep 1, 2013 at 7:54 PM, Trayder Thomas trayder.tho...@monash.edu wrote: It still explodes on a 0.1fs timestep, turning off P-R doesn't seem to have an impact. I've tried being gentle, slowly turning up the force constant and running for 1 ns for each value but as soon as the force constant approaches 100 it crashes. The starting structure was generated with the same restraints, so it is very close. I have tried using slightly different starting structures as well. I've tried running it with only 3 restraints (1 methyl group to 1 hydrogen with the restraints extended by 0.2nm so that all hydrogens are within the restraint distance) and I'm getting a segmentation fault (no LINCS warnings) at 100 steps. It runs fine with any combination of 2 hydrogens restrained, but as soon as I restrain the 3rd one I get a segmentation fault (this occurs with either setting for disre-weighting). So it seems to fair better with more restraints? The more I try to solve this problem the less it makes sense! -Trayder On Fri, Aug 30, 2013 at 6:02 PM, Mark Abraham mark.j.abra...@gmail.com wrote: On Fri, Aug 30, 2013 at 8:56 AM, Trayder trayder.tho...@monash.edu wrote: Hello, I am attempting to simulate a protein-ligand complex using distance restraints to match it to NMR data. The system runs stably without restraints. With restraints it tends to spit out LINCS angle warnings and blow up under most conditions. I'm attempting to use: ; Restraints disre = simple disre-weighting = conservative disre-fc= 1000 It blows up within 100 steps unless: I run on a single core (+gpu) or disre-fc = 100 or disre-weighting = equal If disre-weighting = conservative is causing extreme forces, then I figure it should do the same on 1 core. Not really. MD is chaotic. Small changes in initial conditions lead to different results. If domain decomposition is the problem, then I would think disre-weighting = equal shouldn't work either. I'm stumped... anyone got any ideas? http://www.gromacs.org/Documentation/Terminology/Blowing_Up has the usual suggestions - don't use P-R yet, try a smaller time step, make sure your system is close to the restrained regime (or be extra gentle until it is). Mark Thanks in advance, -Trayder Distance restraints excerpt: ; aiaj typeindex type’ low up1 up2 fac ; 2 symmetric hydrogens 1306 1389 1 10 1 0.0 0.548 1.0 1.0 1306 1396 1 10 1 0.0 0.548 1.0 1.0 ; Diastereotopic methyl groups 1306 1374 1 11 1 0.0 0.654 1.0 1.0 1306 1375 1 11 1 0.0 0.654 1.0 1.0 1306 1376 1 11 1 0.0 0.654 1.0 1.0 1306 1385 1 11 1 0.0 0.654 1.0 1.0 1306 1386 1 11 1 0.0 0.654 1.0 1.0 1306 1387 1 11 1 0.0 0.654 1.0 1.0 Full mdp: ; Run Control integrator = md ; simulation algorithm tinit= 0 dt = 0.002 nsteps = 50 ; ; Output Control nstxout = 20; write coordinates to .trr nstvout = 20; write velocities to .trr nstlog = 1000 ; write energies to .log nstenergy = 4000 ; write energies to .edr nstxtcout = 1000 ; write coordinates to .xtc ; ; Neighbour Searching nstlist = 10 ; update neighbour list ns_type = grid ; neighbour list method pbc = xyz ; periodic boundary conditions rlist = 0.9 ; cut-off for short-range neighbour (nm) cutoff-scheme = verlet ; ; Electrostatics and VdW coulombtype = PME ; type of coulomb interaction
Re: [gmx-users] Distance restraints exploding system
Have you tried with even less restraints? I found systems are not always stable with more than the bare minimum of restraints On Sun, Sep 1, 2013 at 7:54 PM, Trayder Thomas trayder.tho...@monash.eduwrote: It still explodes on a 0.1fs timestep, turning off P-R doesn't seem to have an impact. I've tried being gentle, slowly turning up the force constant and running for 1 ns for each value but as soon as the force constant approaches 100 it crashes. The starting structure was generated with the same restraints, so it is very close. I have tried using slightly different starting structures as well. I've tried running it with only 3 restraints (1 methyl group to 1 hydrogen with the restraints extended by 0.2nm so that all hydrogens are within the restraint distance) and I'm getting a segmentation fault (no LINCS warnings) at 100 steps. It runs fine with any combination of 2 hydrogens restrained, but as soon as I restrain the 3rd one I get a segmentation fault (this occurs with either setting for disre-weighting). So it seems to fair better with more restraints? The more I try to solve this problem the less it makes sense! -Trayder On Fri, Aug 30, 2013 at 6:02 PM, Mark Abraham mark.j.abra...@gmail.com wrote: On Fri, Aug 30, 2013 at 8:56 AM, Trayder trayder.tho...@monash.edu wrote: Hello, I am attempting to simulate a protein-ligand complex using distance restraints to match it to NMR data. The system runs stably without restraints. With restraints it tends to spit out LINCS angle warnings and blow up under most conditions. I'm attempting to use: ; Restraints disre = simple disre-weighting = conservative disre-fc= 1000 It blows up within 100 steps unless: I run on a single core (+gpu) or disre-fc = 100 or disre-weighting = equal If disre-weighting = conservative is causing extreme forces, then I figure it should do the same on 1 core. Not really. MD is chaotic. Small changes in initial conditions lead to different results. If domain decomposition is the problem, then I would think disre-weighting = equal shouldn't work either. I'm stumped... anyone got any ideas? http://www.gromacs.org/Documentation/Terminology/Blowing_Up has the usual suggestions - don't use P-R yet, try a smaller time step, make sure your system is close to the restrained regime (or be extra gentle until it is). Mark Thanks in advance, -Trayder Distance restraints excerpt: ; aiaj typeindex type’ low up1 up2 fac ; 2 symmetric hydrogens 1306 1389 1 10 1 0.0 0.548 1.0 1.0 1306 1396 1 10 1 0.0 0.548 1.0 1.0 ; Diastereotopic methyl groups 1306 1374 1 11 1 0.0 0.654 1.0 1.0 1306 1375 1 11 1 0.0 0.654 1.0 1.0 1306 1376 1 11 1 0.0 0.654 1.0 1.0 1306 1385 1 11 1 0.0 0.654 1.0 1.0 1306 1386 1 11 1 0.0 0.654 1.0 1.0 1306 1387 1 11 1 0.0 0.654 1.0 1.0 Full mdp: ; Run Control integrator = md ; simulation algorithm tinit= 0 dt = 0.002 nsteps = 50 ; ; Output Control nstxout = 20; write coordinates to .trr nstvout = 20; write velocities to .trr nstlog = 1000 ; write energies to .log nstenergy = 4000 ; write energies to .edr nstxtcout = 1000 ; write coordinates to .xtc ; ; Neighbour Searching nstlist = 10 ; update neighbour list ns_type = grid ; neighbour list method pbc = xyz ; periodic boundary conditions rlist = 0.9 ; cut-off for short-range neighbour (nm) cutoff-scheme = verlet ; ; Electrostatics and VdW coulombtype = PME ; type of coulomb interaction rcoulomb= 0.9 ; cut-off distance for coulomb epsilon_r = 1; dielectric constant rvdw= 0.9 ; cut-off for vdw fourierspacing = 0.12 ; maximum grid spacing for FFT pme_order = 4; interpolation order for PME ewald_rtol = 1e-5 ; relative strength of Ewald-shifted DispCorr= EnerPres ; long range dispersion corrections ; ;
Re: [gmx-users] Distance restraints exploding system
It still explodes on a 0.1fs timestep, turning off P-R doesn't seem to have an impact. I've tried being gentle, slowly turning up the force constant and running for 1 ns for each value but as soon as the force constant approaches 100 it crashes. The starting structure was generated with the same restraints, so it is very close. I have tried using slightly different starting structures as well. I've tried running it with only 3 restraints (1 methyl group to 1 hydrogen with the restraints extended by 0.2nm so that all hydrogens are within the restraint distance) and I'm getting a segmentation fault (no LINCS warnings) at 100 steps. It runs fine with any combination of 2 hydrogens restrained, but as soon as I restrain the 3rd one I get a segmentation fault (this occurs with either setting for disre-weighting). So it seems to fair better with more restraints? The more I try to solve this problem the less it makes sense! -Trayder On Fri, Aug 30, 2013 at 6:02 PM, Mark Abraham mark.j.abra...@gmail.comwrote: On Fri, Aug 30, 2013 at 8:56 AM, Trayder trayder.tho...@monash.edu wrote: Hello, I am attempting to simulate a protein-ligand complex using distance restraints to match it to NMR data. The system runs stably without restraints. With restraints it tends to spit out LINCS angle warnings and blow up under most conditions. I'm attempting to use: ; Restraints disre = simple disre-weighting = conservative disre-fc= 1000 It blows up within 100 steps unless: I run on a single core (+gpu) or disre-fc = 100 or disre-weighting = equal If disre-weighting = conservative is causing extreme forces, then I figure it should do the same on 1 core. Not really. MD is chaotic. Small changes in initial conditions lead to different results. If domain decomposition is the problem, then I would think disre-weighting = equal shouldn't work either. I'm stumped... anyone got any ideas? http://www.gromacs.org/Documentation/Terminology/Blowing_Up has the usual suggestions - don't use P-R yet, try a smaller time step, make sure your system is close to the restrained regime (or be extra gentle until it is). Mark Thanks in advance, -Trayder Distance restraints excerpt: ; aiaj typeindex type’ low up1 up2 fac ; 2 symmetric hydrogens 1306 1389 1 10 1 0.0 0.548 1.0 1.0 1306 1396 1 10 1 0.0 0.548 1.0 1.0 ; Diastereotopic methyl groups 1306 1374 1 11 1 0.0 0.654 1.0 1.0 1306 1375 1 11 1 0.0 0.654 1.0 1.0 1306 1376 1 11 1 0.0 0.654 1.0 1.0 1306 1385 1 11 1 0.0 0.654 1.0 1.0 1306 1386 1 11 1 0.0 0.654 1.0 1.0 1306 1387 1 11 1 0.0 0.654 1.0 1.0 Full mdp: ; Run Control integrator = md ; simulation algorithm tinit= 0 dt = 0.002 nsteps = 50 ; ; Output Control nstxout = 20; write coordinates to .trr nstvout = 20; write velocities to .trr nstlog = 1000 ; write energies to .log nstenergy = 4000 ; write energies to .edr nstxtcout = 1000 ; write coordinates to .xtc ; ; Neighbour Searching nstlist = 10 ; update neighbour list ns_type = grid ; neighbour list method pbc = xyz ; periodic boundary conditions rlist = 0.9 ; cut-off for short-range neighbour (nm) cutoff-scheme = verlet ; ; Electrostatics and VdW coulombtype = PME ; type of coulomb interaction rcoulomb= 0.9 ; cut-off distance for coulomb epsilon_r = 1; dielectric constant rvdw= 0.9 ; cut-off for vdw fourierspacing = 0.12 ; maximum grid spacing for FFT pme_order = 4; interpolation order for PME ewald_rtol = 1e-5 ; relative strength of Ewald-shifted DispCorr= EnerPres ; long range dispersion corrections ; ; Restraints disre = simple disre-weighting = conservative disre-fc= 1000 ; ; Temperature Coupling Tcoupl = v-rescale; type of temperature coupling tc-grps = Protein non-Protein ; coupled groups tau_t = .1 .1
[gmx-users] Distance restraints exploding system
Hello, I am attempting to simulate a protein-ligand complex using distance restraints to match it to NMR data. The system runs stably without restraints. With restraints it tends to spit out LINCS angle warnings and blow up under most conditions. I'm attempting to use: ; Restraints disre = simple disre-weighting = conservative disre-fc= 1000 It blows up within 100 steps unless: I run on a single core (+gpu) or disre-fc = 100 or disre-weighting = equal If disre-weighting = conservative is causing extreme forces, then I figure it should do the same on 1 core. If domain decomposition is the problem, then I would think disre-weighting = equal shouldn't work either. I'm stumped... anyone got any ideas? Thanks in advance, -Trayder Distance restraints excerpt: ; aiaj typeindex type’ low up1 up2 fac ; 2 symmetric hydrogens 1306 1389 1 10 1 0.0 0.548 1.0 1.0 1306 1396 1 10 1 0.0 0.548 1.0 1.0 ; Diastereotopic methyl groups 1306 1374 1 11 1 0.0 0.654 1.0 1.0 1306 1375 1 11 1 0.0 0.654 1.0 1.0 1306 1376 1 11 1 0.0 0.654 1.0 1.0 1306 1385 1 11 1 0.0 0.654 1.0 1.0 1306 1386 1 11 1 0.0 0.654 1.0 1.0 1306 1387 1 11 1 0.0 0.654 1.0 1.0 Full mdp: ; Run Control integrator = md ; simulation algorithm tinit= 0 dt = 0.002 nsteps = 50 ; ; Output Control nstxout = 20; write coordinates to .trr nstvout = 20; write velocities to .trr nstlog = 1000 ; write energies to .log nstenergy = 4000 ; write energies to .edr nstxtcout = 1000 ; write coordinates to .xtc ; ; Neighbour Searching nstlist = 10 ; update neighbour list ns_type = grid ; neighbour list method pbc = xyz ; periodic boundary conditions rlist = 0.9 ; cut-off for short-range neighbour (nm) cutoff-scheme = verlet ; ; Electrostatics and VdW coulombtype = PME ; type of coulomb interaction rcoulomb= 0.9 ; cut-off distance for coulomb epsilon_r = 1; dielectric constant rvdw= 0.9 ; cut-off for vdw fourierspacing = 0.12 ; maximum grid spacing for FFT pme_order = 4; interpolation order for PME ewald_rtol = 1e-5 ; relative strength of Ewald-shifted DispCorr= EnerPres ; long range dispersion corrections ; ; Restraints disre = simple disre-weighting = conservative disre-fc= 1000 ; ; Temperature Coupling Tcoupl = v-rescale; type of temperature coupling tc-grps = Protein non-Protein ; coupled groups tau_t = .1 .1 ; T-coupling time constant (ps) ref_t = 310 310 ; reference temperature (K) ; ; Pressure Coupling Pcoupl = parrinello-rahman; type of pressure coupling Pcoupltype = isotropic; pressure coupling geometry tau_p = 2.0 ; p-coupling time constant (ps) compressibility = 4.5e-5 ; compressibiity ref_p = 1.0 ; reference pressure (bar) ; ; Velocity Generation gen_vel = no ; generate initial velocities ; ; Bonds constraints = all-bonds; which bonds to contrain constraint_algorithm= lincs ; algorithm to use lincs_order = 4 lincs_iter = 2 -- View this message in context: http://gromacs.5086.x6.nabble.com/Distance-restraints-exploding-system-tp5010842.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
Re: [gmx-users] Distance restraints exploding system
On Fri, Aug 30, 2013 at 8:56 AM, Trayder trayder.tho...@monash.edu wrote: Hello, I am attempting to simulate a protein-ligand complex using distance restraints to match it to NMR data. The system runs stably without restraints. With restraints it tends to spit out LINCS angle warnings and blow up under most conditions. I'm attempting to use: ; Restraints disre = simple disre-weighting = conservative disre-fc= 1000 It blows up within 100 steps unless: I run on a single core (+gpu) or disre-fc = 100 or disre-weighting = equal If disre-weighting = conservative is causing extreme forces, then I figure it should do the same on 1 core. Not really. MD is chaotic. Small changes in initial conditions lead to different results. If domain decomposition is the problem, then I would think disre-weighting = equal shouldn't work either. I'm stumped... anyone got any ideas? http://www.gromacs.org/Documentation/Terminology/Blowing_Up has the usual suggestions - don't use P-R yet, try a smaller time step, make sure your system is close to the restrained regime (or be extra gentle until it is). Mark Thanks in advance, -Trayder Distance restraints excerpt: ; aiaj typeindex type’ low up1 up2 fac ; 2 symmetric hydrogens 1306 1389 1 10 1 0.0 0.548 1.0 1.0 1306 1396 1 10 1 0.0 0.548 1.0 1.0 ; Diastereotopic methyl groups 1306 1374 1 11 1 0.0 0.654 1.0 1.0 1306 1375 1 11 1 0.0 0.654 1.0 1.0 1306 1376 1 11 1 0.0 0.654 1.0 1.0 1306 1385 1 11 1 0.0 0.654 1.0 1.0 1306 1386 1 11 1 0.0 0.654 1.0 1.0 1306 1387 1 11 1 0.0 0.654 1.0 1.0 Full mdp: ; Run Control integrator = md ; simulation algorithm tinit= 0 dt = 0.002 nsteps = 50 ; ; Output Control nstxout = 20; write coordinates to .trr nstvout = 20; write velocities to .trr nstlog = 1000 ; write energies to .log nstenergy = 4000 ; write energies to .edr nstxtcout = 1000 ; write coordinates to .xtc ; ; Neighbour Searching nstlist = 10 ; update neighbour list ns_type = grid ; neighbour list method pbc = xyz ; periodic boundary conditions rlist = 0.9 ; cut-off for short-range neighbour (nm) cutoff-scheme = verlet ; ; Electrostatics and VdW coulombtype = PME ; type of coulomb interaction rcoulomb= 0.9 ; cut-off distance for coulomb epsilon_r = 1; dielectric constant rvdw= 0.9 ; cut-off for vdw fourierspacing = 0.12 ; maximum grid spacing for FFT pme_order = 4; interpolation order for PME ewald_rtol = 1e-5 ; relative strength of Ewald-shifted DispCorr= EnerPres ; long range dispersion corrections ; ; Restraints disre = simple disre-weighting = conservative disre-fc= 1000 ; ; Temperature Coupling Tcoupl = v-rescale; type of temperature coupling tc-grps = Protein non-Protein ; coupled groups tau_t = .1 .1 ; T-coupling time constant (ps) ref_t = 310 310 ; reference temperature (K) ; ; Pressure Coupling Pcoupl = parrinello-rahman; type of pressure coupling Pcoupltype = isotropic; pressure coupling geometry tau_p = 2.0 ; p-coupling time constant (ps) compressibility = 4.5e-5 ; compressibiity ref_p = 1.0 ; reference pressure (bar) ; ; Velocity Generation gen_vel = no ; generate initial velocities ; ; Bonds constraints = all-bonds; which bonds to contrain constraint_algorithm= lincs ; algorithm to use lincs_order = 4 lincs_iter = 2 -- View this message in context: http://gromacs.5086.x6.nabble.com/Distance-restraints-exploding-system-tp5010842.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org
[gmx-users] Distance restraints
Dear Gromacs users, How to define distance restraints between two molecules(protein and a lipid) in a topology file. Thanks.. -- View this message in context: http://gromacs.5086.x6.nabble.com/Distance-restraints-tp5008421.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
Re: [gmx-users] Distance restraints
You can't - the atoms must be part of the same [moleculetype]. The good news is that a [moleculetype] can have whatever you want in it, so you can have more than one molecule. The bad news is that you'll have to be cunning with renumbering atoms in the merged [moleculetype] and there's no tools that do that. (Or maybe there's a smart-alec trick using the pull code, but I have no idea what.) Mark On Tue, May 21, 2013 at 4:20 PM, Rama ramkishn...@gmail.com wrote: Dear Gromacs users, How to define distance restraints between two molecules(protein and a lipid) in a topology file. Thanks.. -- View this message in context: http://gromacs.5086.x6.nabble.com/Distance-restraints-tp5008421.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 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] Distance restraints
Hi Mark, Is there anyway to define NMR distance restraints in MD simulations to do refinement for the complex structure. On Tue, May 21, 2013 at 10:11 AM, Mark Abraham mark.j.abra...@gmail.comwrote: You can't - the atoms must be part of the same [moleculetype]. The good news is that a [moleculetype] can have whatever you want in it, so you can have more than one molecule. The bad news is that you'll have to be cunning with renumbering atoms in the merged [moleculetype] and there's no tools that do that. (Or maybe there's a smart-alec trick using the pull code, but I have no idea what.) Mark On Tue, May 21, 2013 at 4:20 PM, Rama ramkishn...@gmail.com wrote: Dear Gromacs users, How to define distance restraints between two molecules(protein and a lipid) in a topology file. Thanks.. -- View this message in context: http://gromacs.5086.x6.nabble.com/Distance-restraints-tp5008421.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 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] Distance restraints
Yes. Check out the manual first! Mark On Tue, May 21, 2013 at 5:16 PM, Rama Krishna Koppisetti ramkishn...@gmail.com wrote: Hi Mark, Is there anyway to define NMR distance restraints in MD simulations to do refinement for the complex structure. On Tue, May 21, 2013 at 10:11 AM, Mark Abraham mark.j.abra...@gmail.com wrote: You can't - the atoms must be part of the same [moleculetype]. The good news is that a [moleculetype] can have whatever you want in it, so you can have more than one molecule. The bad news is that you'll have to be cunning with renumbering atoms in the merged [moleculetype] and there's no tools that do that. (Or maybe there's a smart-alec trick using the pull code, but I have no idea what.) Mark On Tue, May 21, 2013 at 4:20 PM, Rama ramkishn...@gmail.com wrote: Dear Gromacs users, How to define distance restraints between two molecules(protein and a lipid) in a topology file. Thanks.. -- View this message in context: http://gromacs.5086.x6.nabble.com/Distance-restraints-tp5008421.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 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] Distance restraints
Hi..,Mark but it is within the same molecule , not in inter-molecules. On Tue, May 21, 2013 at 11:36 AM, Mark Abraham mark.j.abra...@gmail.comwrote: Yes. Check out the manual first! Mark On Tue, May 21, 2013 at 5:16 PM, Rama Krishna Koppisetti ramkishn...@gmail.com wrote: Hi Mark, Is there anyway to define NMR distance restraints in MD simulations to do refinement for the complex structure. On Tue, May 21, 2013 at 10:11 AM, Mark Abraham mark.j.abra...@gmail.com wrote: You can't - the atoms must be part of the same [moleculetype]. The good news is that a [moleculetype] can have whatever you want in it, so you can have more than one molecule. The bad news is that you'll have to be cunning with renumbering atoms in the merged [moleculetype] and there's no tools that do that. (Or maybe there's a smart-alec trick using the pull code, but I have no idea what.) Mark On Tue, May 21, 2013 at 4:20 PM, Rama ramkishn...@gmail.com wrote: Dear Gromacs users, How to define distance restraints between two molecules(protein and a lipid) in a topology file. Thanks.. -- View this message in context: http://gromacs.5086.x6.nabble.com/Distance-restraints-tp5008421.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 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 -- 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] Distance restraints
On 5/21/13 12:53 PM, Rama Krishna Koppisetti wrote: Hi..,Mark but it is within the same molecule , not in inter-molecules. That's what distance restraints are designed for. Please refer to the manual for topology syntax and explanation of the relevant parameters. -Justin On Tue, May 21, 2013 at 11:36 AM, Mark Abraham mark.j.abra...@gmail.comwrote: Yes. Check out the manual first! Mark On Tue, May 21, 2013 at 5:16 PM, Rama Krishna Koppisetti ramkishn...@gmail.com wrote: Hi Mark, Is there anyway to define NMR distance restraints in MD simulations to do refinement for the complex structure. On Tue, May 21, 2013 at 10:11 AM, Mark Abraham mark.j.abra...@gmail.com wrote: You can't - the atoms must be part of the same [moleculetype]. The good news is that a [moleculetype] can have whatever you want in it, so you can have more than one molecule. The bad news is that you'll have to be cunning with renumbering atoms in the merged [moleculetype] and there's no tools that do that. (Or maybe there's a smart-alec trick using the pull code, but I have no idea what.) Mark On Tue, May 21, 2013 at 4:20 PM, Rama ramkishn...@gmail.com wrote: Dear Gromacs users, How to define distance restraints between two molecules(protein and a lipid) in a topology file. Thanks.. -- View this message in context: http://gromacs.5086.x6.nabble.com/Distance-restraints-tp5008421.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 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 -- 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] Distance Restraints
Hi, I'm new to Gromacs. How to convert NMR paramagnetic relaxation enhancement distance restraints into gromacs format in topol.top file for structural MD refinement. --Rama -- View this message in context: http://gromacs.5086.x6.nabble.com/Distance-Restraints-tp5008207.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
Re: [gmx-users] Distance restraints
On 2/14/13 8:35 AM, Divya Sunil wrote: Hello all, I have been trying to apply distance restraints on my protein. I prepared distance restrains using make index and added to topology file. I did it just after executing pdb2gmx. Is this the correct procedure to apply distance restraints? make_ndx doesn't produce restraints, but if you used an index file as input into genrestr -disre, then that's probably correct. The disre.itp file that will be produced will be very generic, with the same restraint distances for everything, so that may or may not be correct for whatever it is you're trying to do. It's easy to manually edit, of course. Bottom line is that a simple test simulation and subsequent measurements will tell you if it is working properly. -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] distance restraints around Zn atom
On 26/07/2012 3:27 PM, Priyanka Shah wrote: Dear all, I want to apply distance restraint between Zn and its coordinating atoms. Zn is supposed to be in octahedral geometry. Zn is making coordination bond with O of hydroxyl group in ligand atom also. Even after several attempts, it seems like destance restraint is not effective because after 1ns MD run, ligand and Zn both move away from their position in opposite directions. I have put following lines in mdp file: title = Protein-ligand complex define = -DPOSRESLIG ; distance restrain from metal disre = simple Distance restraints and position restraints are totally different things. It looks like you need to clean up your work flow in this regard. and added following lines into .top file ; Include Position restraint file #ifdef POSRESLIG #include metalposre.itp #endif where metalporse.itp contains 671 11637 1 3 1 0.09 0.192 0.291 4059 11637 1 7 1 0.11 0.210.311 4070 11637 110 1 0.096 0.196 0.296 1 4071 11637 112 1 0.094 0.1950.295 1 11637 11662 114 1 0.12 0.230.32 1 where 671 - OD2 of Asp45, 4059 - NE2 of Hid267, 4070 - OD1 of Asp268, 4071 - OD2 of Asp268, 11637 - Zn and 11662 - O of Lig. looking for suggestions. Your .log and .edr files will have contributions from restraint violations, which you can use as a necessary-but-not-sufficient test for things working correctly. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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] distance restraints around Zn atom
Dear all, I want to apply distance restraint between Zn and its coordinating atoms. Zn is supposed to be in octahedral geometry. Zn is making coordination bond with O of hydroxyl group in ligand atom also. Even after several attempts, it seems like destance restraint is not effective because after 1ns MD run, ligand and Zn both move away from their position in opposite directions. I have put following lines in mdp file: title = Protein-ligand complex define = -DPOSRESLIG ; distance restrain from metal disre = simple and added following lines into .top file ; Include Position restraint file #ifdef POSRESLIG #include metalposre.itp #endif where metalporse.itp contains 671 11637 1 3 1 0.09 0.192 0.291 4059 11637 1 7 1 0.11 0.210.311 4070 11637 110 1 0.096 0.196 0.296 1 4071 11637 112 1 0.094 0.1950.295 1 11637 11662 114 1 0.12 0.230.32 1 where 671 - OD2 of Asp45, 4059 - NE2 of Hid267, 4070 - OD1 of Asp268, 4071 - OD2 of Asp268, 11637 - Zn and 11662 - O of Lig. looking for suggestions. Thank you Priyanka Shah Central Drug Research Institute Lucknow, India -- Let spontaneity guide you! -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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] Distance Restraints of 3 atoms
Dear Gmx Users, I want use distance restraints of 3 atoms belonging to 3 different moleculetypes. In this case shall I create and index file of those atoms and then use: genrestr -f X.pdb -n index.ndx -disre -o disre.itp ? Under which topology file shall I add: #ifdef DISRES # include 'disre.itp' Please help, Steven -- 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] Distance restraints not working
Dear all, I am attempting to keep a Zn ion in place in a zinc finger motif using distance restraints to the coordinating cysteine residues. The zinc is structural and not catalytic, and it was suggested from this list that using distance restraints should suffice without the need for reparameterization. Unfortunately after several tries the distance restraints don't appear to be applied after 100 ps of isothermal-isochoric equilibration, however it did seem to work for the minimization step. My topology file contains the following: #ifdef DISRES [ distance_restraints ] ; ai aj type index typeâ low up1 up2 fac 13082 5576 10 1 0.0 0.23 0.3 1.0 13082 5604 11 1 0.0 0.23 0.3 1.0 13082 5959 12 1 0.0 0.23 0.3 1.0 13082 5993 13 1 0.0 0.20 0.3 1.0 #endif and my .mdp file has the following two lines inserted: define = -DDISRES ; distance restrain the protein disre = simple; Enable Distance Restraints I first attempted to use small factors to multiply the restraints, 1, 2, 10, but nothing seemed to be working so I just put an extreme value of 10,000 to ensure the energy contribution from the restraints would dominate and keep the zinc in place, but that still didn't seem to do the trick which makes me think that there's some other error I'm missing. I checked my .gro file to ensure that the atom indices were correct and they are. I also have ensured that the zinc ion and coordinating cysteines are part of the same chain. The zinc appears to move by about 4 Å to be coordinated by a nearby glutamate instead. Any ideas on why the restraints don't seem to be working? Thanks, Tom -- Thomas D. Grant Graduate Research Assistant Hauptman-Woodward Medical Research Institute 700 Ellicott St. Buffalo, NY 14203 -- 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] Distance restraints not working
On 5/22/12 9:25 PM, Thomas Grant wrote: Dear all, I am attempting to keep a Zn ion in place in a zinc finger motif using distance restraints to the coordinating cysteine residues. The zinc is structural and not catalytic, and it was suggested from this list that using distance restraints should suffice without the need for reparameterization. Unfortunately after several tries the distance restraints don't appear to be applied after 100 ps of isothermal-isochoric equilibration, however it did seem to work for the minimization step. My topology file contains the following: #ifdef DISRES [ distance_restraints ] ; ai aj type index typeâ low up1 up2 fac 13082 5576 10 1 0.0 0.23 0.3 1.0 13082 5604 11 1 0.0 0.23 0.3 1.0 13082 5959 12 1 0.0 0.23 0.3 1.0 13082 5993 13 1 0.0 0.20 0.3 1.0 #endif and my .mdp file has the following two lines inserted: define = -DDISRES ; distance restrain the protein disre = simple; Enable Distance Restraints I first attempted to use small factors to multiply the restraints, 1, 2, 10, but nothing seemed to be working so I just put an extreme value of 10,000 to ensure the energy contribution from the restraints would dominate and keep the zinc in place, but that still didn't seem to do the trick which makes me think that there's some other error I'm missing. I checked my .gro file to ensure that the atom indices were correct and they are. I also have ensured that the zinc ion and coordinating cysteines are part of the same chain. The zinc appears to move by about 4 Å to be coordinated by a nearby glutamate instead. Any ideas on why the restraints don't seem to be working? There are a few possibilities. 1. Numbering in [distance_restraints] is not based on .gro numbering. The atom numbers supplied are only relevant within the [moleculetype] to which they belong, much like [position_restraints]. Also make sure that the [distance_restraints] block is in the correct location in the topology. 2. You've omitted the dihre_fc keyword, though it is set to 1000 by default. Check the mdout.mdp file or your .tpr file to ensure that you have a sensible value here. Setting values of fac that high are unnecessary. -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] distance restraints
Dear all I 'd like to do NOE distance restraints; according to the chapter 4 of the manual; I should specify a section for [ distance_restraints] : [ distance_restraints ] ; ai aj type index type’ low up1 up2 fac 10 161010.00.30.41.0 10 281110.00.30.41.0 10 461110.00.30.41.0 16 221210.00.30.42.5 16 341310.00.50.61.0 . althought I've studied the manual, it is still unclear to me, that how is the index column defined? what are the numbers (0,1,2,3) implying? what about the low, up1,up2, fac columns? Thank you in advance B.Mehrazma -- 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] distance restraints
On 5/17/12 2:51 AM, Banafsheh Mehrazma wrote: Dear all I 'd like to do NOE distance restraints; according to the chapter 4 of the manual; I should specify a section for [ distance_restraints] : [ distance_restraints ] ; ai aj type index type’ low up1 up2 fac 10 161010.00.30.41.0 10 281110.00.30.41.0 10 461110.00.30.41.0 16 221210.00.30.42.5 16 341310.00.50.61.0 . althought I've studied the manual, it is still unclear to me, that how is the index column defined? what are the numbers (0,1,2,3) implying? what about the low, up1,up2, fac columns? All of this information is in the manual, section 4.3.4, under the heading Using distance restraints. With respect to indices: The type column should always be 1. As explained in sec. 4.3.4, multiple distances can contribute to a single NOE signal. In the topology this can be set using the index column. In our example, the restraints 10-28 and 10-46 both have index 1, therefore they are treated simultaneously. With respect to low, up1, and up2: The columns low, up1, and up2 hold the values of r0, r1, and r2 from eqn. 4.77. For fac: In some cases it can be useful to have different force constants for some restraints; this is controlled by the column fac. The force constant in the parameter file is multiplied by the value in the column fac for each restraint. -Justin -- Justin A. Lemkul, Ph.D. 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] distance restraints fails
Dear gmx users, I tried to apply distance restraints to my system, but I found that it failed because the distance between the restraints atoms in the last frame is bigger than what we want. Here are the parameters for distance restraints in the topology file: [ distance_restraints ] ; ai aj type index type’ low up1 up2 fac 8 192 1 0 1 0.0 0.3 0.4 2.5 18 203 1 0 1 0.0 0.3 0.4 2.5 20 205 1 0 1 0.0 0.3 0.4 2.5 and also I tried this (added four other distance restraints in the same two groups): [ distance_restraints ] ; ai aj type index type’ low up1 up2 fac 7 193 1 0 1 0.0 0.3 0.4 2.5 8 192 1 0 1 0.0 0.3 0.4 2.5 11 195 1 0 1 0.0 0.3 0.4 2.5 18 202 1 0 1 0.0 0.3 0.4 2.5 20 202 1 0 1 0.0 0.3 0.4 2.5 18 203 1 0 1 0.0 0.3 0.4 2.5 20 205 1 0 1 0.0 0.3 0.4 2.5 I am sure that the atom numbers are right. And the following lines are the mdp file I used: title = PDXN of Abeta in H2O ;cpp = /lib/cpp ; prepocessor of the current machine define = ;-DPOSRES integrator = md ; molecular dynamics algorithm tinit = 0.0 ; start time and timestep in ps dt = 0.002; time step in ps nsteps = 100 ; number of steps for 1000 ns run emtol = 100; convergence criterion emstep = 0.05 ; intial step size nstlist = 0 ; step frequency for updating neighbour list ns_type = simple ;grid ; method for neighbour searching (?) nstxout = 5000 ; frequency for writing coords to output .trr file nstvout = 0 ; frequency for writing velocities to output...should be same as nstxout nstfout = 0; frequency for writing forces to output nstlog = 5000 ; frequency for writing energies to log file nstenergy = 5000 ; frequency for writing energies to energy file nstxtcout = 5000 ; frequency for writing coords to xtc traj xtc_grps= system ; group(s) whose coords are to be written in xtc traj energygrps = system ; group(s) whose energy is to be written in energy file ;distance restraints disre = simple disre_fc= 2 ; for the force, I tried 3000, 6000, 1 and 15000, but all the tests failed disre_mixed = yes disre_weighting = equal disre_tau = 10 nstdisreout = 100 ; comm_mode = angular nstcomm = 10 comm_grps = system ; pbc = no ;xyz ; use pbc rlist = 0 ;1.4 ; cutoff lengths (nm) epsilon_r = 1.0 ; Dielectric constant (DC) for twin-range or DC of reaction field niter = 100 ; Some thingies for future use fourierspacing= 0.16 fourier_nx = 30 fourier_ny = 30 fourier_nz = 30 coulombtype = Cut-off ; truncation for minimisation, with large cutoff rcoulomb= 0 ;1.4 rcoulomb-switch = 0 vdw-type = Cut-off ; truncation for minimisation, with large cutoff rvdw-switch = 0 rvdw = 0 ; 1.4 ; cut-off lengths ;pme_order= 6; EWALD/PME/PPPM parameters ;ewald_rtol = 1e-05 ;ewald_geometry = 3d epsilon_surface = 0 optimize_fft = yes Free energy control stuff free_energy = yes init_lambda = 0.0 delta_lambda = 0 sc_alpha =0.5 sc-power =1.0 sc-sigma = 0.3 ;nstcomm = 0; number of steps for centre of mass motion removal (in vacuo only!) Tcoupl = V-rescale ;Berendsen tc_grps = system ;Other Water_and_ions tau_t = 0.5 ; 0.5 ref_t = 300 ; 300 Pcoupl = no ;Pcoupltype = Isotropic ;tau_p = 1.0 1.0 1.0 ;ref_p = 1.0 1.0 1.0 ;compressibility = 4.5e-5 ; compressibility annealing = no ; SIMULATED ANNEALING CONTROL ;zero_temp_time = 0; Time at which temperature should be zero (ps) gen_vel = yes gen_temp= 300 gen_seed= -1 constraints = all-bonds ; OPTIONS FOR BOND CONSTRAINTS constraint-algorithm = Lincs ; Type of constraint algorithm lincs_order = 4; Highest order in the expansion of the constraint coupling matrix lincs_warnangle = 30 ; Lincs will write a warning to the stderr if in one step a bond rotates ; over more degrees than unconstrained-start = no ; Do not constrain the start configuration ;Shake-SOR= no ; Use successive overrelaxation to
Re: [gmx-users] distance restraints fails
On 13/04/2012 3:08 AM, Qinghua Liao wrote: Dear gmx users, I tried to apply distance restraints to my system, but I found that it failed because the distance between the restraints atoms in the last frame is bigger than what we want. Distance restraints aren't magic. There has to be an accessible simulation path from your initial conditions to one that satisfies the restraints. So far you haven't found one - there need not be one. Mark Here are the parameters for distance restraints in the topology file: [ distance_restraints ] ; ai aj type index type' low up1 up2 fac 8 192 1 0 1 0.0 0.3 0.4 2.5 18 203 1 0 1 0.0 0.3 0.4 2.5 20 205 1 0 1 0.0 0.3 0.4 2.5 and also I tried this (added four other distance restraints in the same two groups): [ distance_restraints ] ; ai aj type index type' low up1 up2 fac 7 193 1 0 1 0.0 0.3 0.4 2.5 8 192 1 0 1 0.0 0.3 0.4 2.5 11 195 1 0 1 0.0 0.3 0.4 2.5 18 202 1 0 1 0.0 0.3 0.4 2.5 20 202 1 0 1 0.0 0.3 0.4 2.5 18 203 1 0 1 0.0 0.3 0.4 2.5 20 205 1 0 1 0.0 0.3 0.4 2.5 I am sure that the atom numbers are right. And the following lines are the mdp file I used: title = PDXN of Abeta in H2O ;cpp = /lib/cpp ; prepocessor of the current machine define = ;-DPOSRES integrator = md ; molecular dynamics algorithm tinit = 0.0 ; start time and timestep in ps dt = 0.002; time step in ps nsteps = 100 ; number of steps for 1000 ns run emtol = 100; convergence criterion emstep = 0.05 ; intial step size nstlist = 0 ; step frequency for updating neighbour list ns_type = simple ;grid ; method for neighbour searching (?) nstxout = 5000 ; frequency for writing coords to output .trr file nstvout = 0 ; frequency for writing velocities to output...should be same as nstxout nstfout = 0; frequency for writing forces to output nstlog = 5000 ; frequency for writing energies to log file nstenergy = 5000 ; frequency for writing energies to energy file nstxtcout = 5000 ; frequency for writing coords to xtc traj xtc_grps= system ; group(s) whose coords are to be written in xtc traj energygrps = system ; group(s) whose energy is to be written in energy file ;distance restraints disre = simple disre_fc= 2 ; for the force, I tried 3000, 6000, 1 and 15000, but all the tests failed disre_mixed = yes disre_weighting = equal disre_tau = 10 nstdisreout = 100 ; comm_mode = angular nstcomm = 10 comm_grps = system ; pbc = no ;xyz ; use pbc rlist = 0 ;1.4 ; cutoff lengths (nm) epsilon_r = 1.0 ; Dielectric constant (DC) for twin-range or DC of reaction field niter = 100 ; Some thingies for future use fourierspacing = 0.16 fourier_nx = 30 fourier_ny = 30 fourier_nz = 30 coulombtype = Cut-off ; truncation for minimisation, with large cutoff rcoulomb= 0 ;1.4 rcoulomb-switch = 0 vdw-type = Cut-off ; truncation for minimisation, with large cutoff rvdw-switch = 0 rvdw = 0 ; 1.4 ; cut-off lengths ;pme_order= 6; EWALD/PME/PPPM parameters ;ewald_rtol = 1e-05 ;ewald_geometry = 3d epsilon_surface = 0 optimize_fft = yes Free energy control stuff free_energy = yes init_lambda = 0.0 delta_lambda = 0 sc_alpha =0.5 sc-power =1.0 sc-sigma = 0.3 ;nstcomm = 0; number of steps for centre of mass motion removal (in vacuo only!) Tcoupl = V-rescale ;Berendsen tc_grps = system ;Other Water_and_ions tau_t = 0.5 ; 0.5 ref_t = 300 ; 300 Pcoupl = no ;Pcoupltype = Isotropic ;tau_p = 1.0 1.0 1.0 ;ref_p = 1.0 1.0 1.0 ;compressibility = 4.5e-5 ; compressibility annealing = no ; SIMULATED ANNEALING CONTROL ;zero_temp_time = 0; Time at which temperature should be zero (ps) gen_vel = yes gen_temp= 300 gen_seed= -1 constraints = all-bonds ; OPTIONS FOR BOND CONSTRAINTS constraint-algorithm = Lincs ; Type of constraint algorithm lincs_order = 4; Highest order in the expansion of the constraint coupling matrix lincs_warnangle
Re: [gmx-users] Distance Restraints on Protein - possible at all?
On 22/02/2012 11:17 AM, NG HUI WEN wrote: *From:*NG HUI WEN *Sent:* Sunday, February 19, 2012 1:19 PM *To:* gmx-users@gromacs.org *Subject:* Distance Restraints on Protein - possible at all? Dear gmxusers, I have been trying to apply distance restraints on my protein but have been unsuccessful thus far. For what purpose? I have consulted the user forum previously and with some much-appreciated help I have managed to get my simulation (with distance restraints applied) to run. However, the joy did not last long as the simulation crashed very quickly (after ~40-50ps). Do they run with no restraints? P-R P-coupling is known to be unsuitable for equilibration (see manual), so that might be a factor here. Mark -- 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] Distance Restraints on Protein - possible at all?
Dear Mark, Thanks for contributing your ideas and suggestions, really appreciate it. The reason I am playing with distance restraints on my protein is because I am interested to see the effects of equilibrating a protein in membrane using the two different restraint methods i.e. distance vs. position. Yes, without distance restraint (i.e. removing disre = simple in the mdp) will allow the simulation to run to completion very smoothly. I will give Berendsen pressure coupling a shot and see how it goes. However, prior to applying distance restraint on my protein, I have ran 5ns of position restraint simulation (with P-R coupling) and there weren't any complaints/problems. Many thanks again for your help. Cheers, Huiwen From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Mark Abraham Sent: Thursday, February 23, 2012 9:48 AM To: Discussion list for GROMACS users Subject: Re: [gmx-users] Distance Restraints on Protein - possible at all? On 22/02/2012 11:17 AM, NG HUI WEN wrote: From: NG HUI WEN Sent: Sunday, February 19, 2012 1:19 PM To: gmx-users@gromacs.orgmailto:gmx-users@gromacs.org Subject: Distance Restraints on Protein - possible at all? Dear gmxusers, I have been trying to apply distance restraints on my protein but have been unsuccessful thus far. For what purpose? I have consulted the user forum previously and with some much-appreciated help I have managed to get my simulation (with distance restraints applied) to run. However, the joy did not last long as the simulation crashed very quickly (after ~40-50ps). Do they run with no restraints? P-R P-coupling is known to be unsuitable for equilibration (see manual), so that might be a factor here. Mark This message and any attachment are intended solely for the addressee and may contain confidential information. If you have received this message in error, please send it back to me, and immediately delete it. Please do not use, copy or disclose the information contained in this message or in any attachment. Any views or opinions expressed by the author of this email do not necessarily reflect the views of the University of Nottingham. This message has been checked for viruses but the contents of an attachment may still contain software viruses which could damage your computer system: you are advised to perform your own checks. Email communications with the University of Nottingham may be monitored as permitted by UK Malaysia legislation. -- 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] Distance Restraints on Protein - possible at all?
From: NG HUI WEN Sent: Sunday, February 19, 2012 1:19 PM To: gmx-users@gromacs.org Subject: Distance Restraints on Protein - possible at all? Dear gmxusers, I have been trying to apply distance restraints on my protein but have been unsuccessful thus far. I have consulted the user forum previously and with some much-appreciated help I have managed to get my simulation (with distance restraints applied) to run. However, the joy did not last long as the simulation crashed very quickly (after ~40-50ps). Below is an account of the attempts I made. Please bear with me as it is quite lenghty. I have tried to resolve the problem (but all to no avail) by : a)changing the distance restraint group from CA to backbone - in case the protein is too floppy b)fc from 1 to 1000 (default) to 0 - in order to check if the problem comes from the strenght of restraints Below sum up what I had done: 1) prepare disre.itp file genrestr -f posre_NVT_rep1.gro -o ca_disre.itp -disre 2) mdp looks: title = NPT define = -DDISRES integrator = md nsteps = 50 dt = 0.002 nstxout = 5 nstvout = 5 nstenergy = 2500 nstlog = 500 nstxtcout = 5 continuation = yes constraint_algorithm = lincs constraints = all-bonds lincs_iter = 1 lincs_order = 4 ns_type = grid nstlist = 10 rlist = 1.2 rcoulomb = 1.2 rvdw = 1.2 coulombtype = PME pme_order = 4 fourierspacing = 0.12 tcoupl = v-rescale tc-grps = Protein POPC WATER_SOL_CL tau_t = 0.1 0.1 0.1 ref_t = 310 310 310 pcoupl = Parrinello-Rahman pcoupltype = semiisotropic tau_p = 1.0 ref_p = 1.0 1.0 compressibility = 4.5e-5 4.5e-5 pbc = xyz DispCorr = EnerPres gen_vel = no nstcomm = 10 comm-mode = Linear comm-grps = Protein_POPC WATER_SOL_CL energygrps = Protein POPC WATER_SOL_CL ; DISRE parameters disre = simple disre-fc = (i)1/ (ii)1000 / (iii) 0 3) top file looks like this: ; Include forcefield parameters #include gromos53a6_lipid.ff/forcefield.itp ;Include Protein Topology #include A2a.itp ; Include Position restraint file #ifdef DISRES #include ca_disre.itp #endif ; #ifdef POSRES #include posre.itp #endif ; ;Include POPC topology #include popc.itp #ifdef LIPID_POSRES #include lipid_posre.itp #endif ;Include water topology #include gromos53a6_lipid.ff/spc.itp #ifdef POSRES_WATER ; Position restraint for each water oxygen [ position_restraints ] ; i funct fcx fcy fcz 1 1 1000 1000 1000 #endif ; Include topology for ions #include gromos53a6_lipid.ff/ions.itp [ system ] ; Name POPC and protein in water [ molecules ] ; Compound #mols Protein_chain_X 1 POPC 327 SOL 24767 CL 11 4) prepare .tpr file grompp -f NPT_disres.mdp -c posre_NPT_rep1.gro -n index.ndx -p merged.top -t posre_NPT_rep1.cpt -o disre.tpr 5) mdrun mdrun-mpi -v -s disre.tpr -deffnm disre -pd The following are snippets of the output and log file before the simulations blew up: i)fc= 1 step 21300, will finish Wed Feb 15 11:07:18 2012 step 21400, will finish Wed Feb 15 11:08:38 2012 Step 21481, time 42.962 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.007728, max 0.339710 (between atoms 9 and 11) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length Step 21482, time 42.964 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.022906, max 0.865028 (between atoms 12 and 16) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 16 17 31.6 0.1212 0.1447 0.1230 12 16 104.7 0.1266 0.0207 0.1530 9 11 110.7 0.0878 0.0397 0.1330 Wrote pdb files with previous and current coordinates Step 21483, time 42.966 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.009368, max 0.641094 (between atoms 9 and 11) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 1 2 33.3 0.0928 0.0961 0.1000 18 20 34.2 0.1474 0.1635 0.1470 16 18 60.0 0.1842 0.1310 0.1330 16 17 64.8 0.1447 0.1264 0.1230 14 15 30.4 0.0979 0.1525 0.1530 11 15 77.5 0.2435 0.1147 0.1470 11 12 34.5 0.2609 0.1633 0.1470 9 11 95.3 0.0397 0.2183 0.1330 Wrote pdb files with previous and current coordinates Step 21484, time 42.968 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.013088, max 0.518530 (between atoms 12 and 16) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 1 2 40.0 0.0961 0.0952 0.1000 18 19 59.6 0.0996 0.0782 0.1000 ii) fc= 1000 (default) step 21200, will finish Thu Feb 16 02:22:10 2012 step 21300, will finish Thu Feb 16 02:22:09 2012 step 21400, will finish Thu Feb 16 02:22:07 2012 Step 21481, time 42.962 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.007728, max 0.339710 (between atoms 9 and 11) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length Step 21482, time 42.964 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.022906, max 0.865028
[gmx-users] distance restraints for atoms on 2 chains
Hi, I have 5 chains in my Protein. I want to apply distance restraints for doing Umbrella Sampling for 2 atoms on different chains. Is there a way to do this since the two chains have separater itp files. Pooja -- Quaerendo Invenietis-Seek and you shall discover. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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] Distance Restraints: Inconsistent Shifts, LINCS Warnings, Number of grid cells is zero, XTC error
What do you mean by mutually inconsistent? From what I understand, they aren't. Also, [bonds] type 6 won't work for what I want, since I don't want to keep the molecules at a fixed distance but to prevent them from coming closer, i.e. I want a potential that depends on the distance between the atoms. Testing the distance restraints can be quite exhaustive when you have about 160 restraints, and I am considering just the test case I'm trying, not the actual system which will have some more organic molecules, which will lead to a greater amount of combination of restraints... Thanks, João On Fri, Oct 9, 2009 at 12:51 AM, Mark Abraham mark.abra...@anu.edu.auwrote: João M. Damas wrote: Gromacs users, I have a small test system of about 2500 atoms which consists on a few organic molecules in a box of water. I'm trying to use distance restraints to keep each molecule apart from each other and I've failed until now. I'll start by saying that the simulation runs smoothly without using distance restraints and that I've created a single molecule topology that describes all organic molecules, allowing the use of distance restraints. By applying just one distance restraint between two atoms of different molecules, the simulation still runs without problems. When I apply all the distance restraints I want, the system crashes in the first few steps with an XTC error, which is preceded by a few inconsistent shifts and some LINCS warnings. Varying the number of restraints that I use, makes the crash happen at later steps (500ish), meanwhile giving a lot of inconsistent shifts before crashing with a fatal error: Number of grid cells is zero. I know it seems I'm experimenting blindly, but varying the number of restraints was the first that occurred to me. I've searched the list for similar problems and tried a few more tests. I've turned off LINCS and reduced the time step and it didn't solve the problem, the box blew up after a few steps due to pressure problems. Since it could be a PBC problem, I tried to increase the size of the box, but it didn't solve the problem. Turning of PBC did solve the problem, but I really need PBC. I've also changed the low, up1 and up2 to values inferior to half the box size (I don't even care about the up1 and up2 values in this application, and I was setting them to 5.0 nm before), but it didn't solve the problem either. I'm a little on a dead end here and I was hoping anyone could give me some insight. By the way, I'm using GROMACS 4. The simplest explanation is that your sets of distance restraints are mutually inconsistent. This destabilizes the system and eventually leads to your symptoms. Consider using [bonds] type 6, per advice of manual section 4.3.4. Either way, if you add these restraints one by one after testing that the previous set seemed to work OK (didn't crash, trajectory looks right), you may uncover your issue. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- João M. Damas PhD Student Protein Modelling Group ITQB-UNL, Oeiras, Portugal Tel:+351-214469613 ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Distance Restraints: Inconsistent Shifts, LINCS Warnings, Number of grid cells is zero, XTC error
João M. Damas wrote: What do you mean by mutually inconsistent? From what I understand, they aren't. I mean a set for which there is no molecular arrangement that satisfies. Also, [bonds] type 6 won't work for what I want, since I don't want to keep the molecules at a fixed distance but to prevent them from coming closer, i.e. I want a potential that depends on the distance between the atoms. Testing the distance restraints can be quite exhaustive when you have about 160 restraints, and I am considering just the test case I'm trying, not the actual system which will have some more organic molecules, which will lead to a greater amount of combination of restraints... #ifdef is your friend here... [ distance_restraints ] set to test now #ifdef BLAHBLAH set to test later #endif Now you just move the #ifdef to rearrange your test cases. I might start with an even smaller test case until you prove you can deal with both the input formatting issues and the physics issues with it. Testing will be faster, for starters. Mark On Fri, Oct 9, 2009 at 12:51 AM, Mark Abraham mark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.au wrote: João M. Damas wrote: Gromacs users, I have a small test system of about 2500 atoms which consists on a few organic molecules in a box of water. I'm trying to use distance restraints to keep each molecule apart from each other and I've failed until now. I'll start by saying that the simulation runs smoothly without using distance restraints and that I've created a single molecule topology that describes all organic molecules, allowing the use of distance restraints. By applying just one distance restraint between two atoms of different molecules, the simulation still runs without problems. When I apply all the distance restraints I want, the system crashes in the first few steps with an XTC error, which is preceded by a few inconsistent shifts and some LINCS warnings. Varying the number of restraints that I use, makes the crash happen at later steps (500ish), meanwhile giving a lot of inconsistent shifts before crashing with a fatal error: Number of grid cells is zero. I know it seems I'm experimenting blindly, but varying the number of restraints was the first that occurred to me. I've searched the list for similar problems and tried a few more tests. I've turned off LINCS and reduced the time step and it didn't solve the problem, the box blew up after a few steps due to pressure problems. Since it could be a PBC problem, I tried to increase the size of the box, but it didn't solve the problem. Turning of PBC did solve the problem, but I really need PBC. I've also changed the low, up1 and up2 to values inferior to half the box size (I don't even care about the up1 and up2 values in this application, and I was setting them to 5.0 nm before), but it didn't solve the problem either. I'm a little on a dead end here and I was hoping anyone could give me some insight. By the way, I'm using GROMACS 4. The simplest explanation is that your sets of distance restraints are mutually inconsistent. This destabilizes the system and eventually leads to your symptoms. Consider using [bonds] type 6, per advice of manual section 4.3.4. Either way, if you add these restraints one by one after testing that the previous set seemed to work OK (didn't crash, trajectory looks right), you may uncover your issue. Mark ___ gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- João M. Damas PhD Student Protein Modelling Group ITQB-UNL, Oeiras, Portugal Tel:+351-214469613 ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at
[gmx-users] Distance Restraints: Inconsistent Shifts, LINCS Warnings, Number of grid cells is zero, XTC error
Gromacs users, I have a small test system of about 2500 atoms which consists on a few organic molecules in a box of water. I'm trying to use distance restraints to keep each molecule apart from each other and I've failed until now. I'll start by saying that the simulation runs smoothly without using distance restraints and that I've created a single molecule topology that describes all organic molecules, allowing the use of distance restraints. By applying just one distance restraint between two atoms of different molecules, the simulation still runs without problems. When I apply all the distance restraints I want, the system crashes in the first few steps with an XTC error, which is preceded by a few inconsistent shifts and some LINCS warnings. Varying the number of restraints that I use, makes the crash happen at later steps (500ish), meanwhile giving a lot of inconsistent shifts before crashing with a fatal error: Number of grid cells is zero. I know it seems I'm experimenting blindly, but varying the number of restraints was the first that occurred to me. I've searched the list for similar problems and tried a few more tests. I've turned off LINCS and reduced the time step and it didn't solve the problem, the box blew up after a few steps due to pressure problems. Since it could be a PBC problem, I tried to increase the size of the box, but it didn't solve the problem. Turning of PBC did solve the problem, but I really need PBC. I've also changed the low, up1 and up2 to values inferior to half the box size (I don't even care about the up1 and up2 values in this application, and I was setting them to 5.0 nm before), but it didn't solve the problem either. I'm a little on a dead end here and I was hoping anyone could give me some insight. By the way, I'm using GROMACS 4. Thanks in advance and sorry if I sounded confusing. Best regards, João -- João M. Damas PhD Student Protein Modelling Group ITQB-UNL, Oeiras, Portugal Tel:+351-214469613 ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] distance restraints in Gromacs 4.0.4
Dear users I have found a problem for the distance constraint in the version 4.0.4 of gromacs. I am trying to simulate a water droplet around an ion. To do that I use a distance restraint armonic potential (pag.66, manual version 4). During my simulation the shape of my sphere fluctuating too much and many molecules leave the sphere even if the restoring force is big (I use for restraint armonic potential a constant k=1e4 KJ mol^-1 nm^-2 ). The problem disappear if I run the exactly same simulation with gromacs 3.3.3.:the spherical shape is always conserve and no molecules leave the sphere. Furthermore, if I am trying to run droplet larger than 1.0 nm radius (e.g. 1.6 nm). These simulation at a certain point stop, giving me the following error ** glibc detected *** Dmdrun: munmap_chunk(): invalid pointer: 0x00a72bd0 *** The same simulation in the version 3.3.3 runs without any problem. Do you know what kind of problem could be? Has the version 4.0.4 some problems with distance restrains? Thank you in advance for any help or suggestion Ivan Gladich -- --- Ivan Gladich Dreyfus Postdoctoral Fellow Department of Chemistry Purdue University 560 Oval Drive, box 140 West Lafayette IN 47906 USA Room: 265C Tel:765-494-5225 e-mail: iglad...@purdue.edu web page: http://web.ics.purdue.edu/~igladich/ ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] distance restraints for alpha helix
Dear all, I am trying to rebuild the alpha helix of one the chains which got destroyed during the simulation. I found that we can do that by distance restraints. So my question what is a better way of distance restraints i.e should I restrain the hydrogen bonds of the helix or any particular bond distances. I was not clear when I read the chapter 4 in manual, what type' should I use for this, are these parameterized anywhere because the manual says type' should be 1 for bonds but for hydrogen bonds it varies from 0-2. I found an exercise by David van der Spoel http://www.csc.fi/english/research/sciences/chemistry/courses/gmx2004/exercises/index_html but could not access the files, so I was not clear what atoms did he use for restraints. Thank you abhigna ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] distance restraints and domain decomposition
Hi, Is this the only output you got? There is no error message at all? If there was no error message and you get the error quickly (i.e. not after hours of simulations), please file a bugzilla entry, give the exact command line of mpirun and mdrun and attach your tpr file. Berk Date: Fri, 5 Dec 2008 14:33:30 -0500 From: [EMAIL PROTECTED] To: gmx-users@gromacs.org Subject: [gmx-users] distance restraints and domain decomposition Hi All, I am trying to run a simulation on a 13 residue peptide fragment with distance restraints in parallel and I'm getting a fatal error when I try to implement mdrun. Here is my nohup.out file: :-) G R O M A C S (-: Giving Russians Opium May Alter Current Situation :-) VERSION 4.0 (-: Written by David van der Spoel, Erik Lindahl, Berk Hess, and others. Copyright (c) 1991-2000, University of Groningen, The Netherlands. Copyright (c) 2001-2008, The GROMACS development team, check out http://www.gromacs.org for more information. This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version. :-) mdrunmpi (-: Option Filename Type Description -s md.tpr InputRun input file: tpr tpb tpa -o md.trr Output Full precision trajectory: trr trj cpt -x md.xtc Output, Opt! Compressed trajectory (portable xdr format) -cpi state.cpt Input, Opt. Checkpoint file -cpo state.cpt Output, Opt. Checkpoint file -c md.gro Output Structure file: gro g96 pdb -e md.edr Output Energy file: edr ene -g md.log Output Log file -dgdl dgdl.xvg Output, Opt. xvgr/xmgr file -fieldfield.xvg Output, Opt. xvgr/xmgr file -tabletable.xvg Input, Opt. xvgr/xmgr file -tablep tablep.xvg Input, Opt. xvgr/xmgr file -tableb table.xvg Input, Opt. xvgr/xmgr file -rerunrerun.xtc Input, Opt. Trajectory: xtc trr trj gro g96 pdb cpt -tpitpi.xvg Output, Opt. xvgr/xmgr file -tpid tpidist.xvg Output, Opt. xvgr/xmgr file -eisam.edi Input, Opt. ED sampling input -eosam.edo Output, Opt. ED sampling output -j wham.gct Input, Opt. General coupling stuff -jobam.gct Output, Opt. General coupling stuff -ffout gct.xvg Output, Opt. xvgr/xmgr file -devout deviatie.xvg Output, Opt. xvgr/xmgr file -runav runaver.xvg Output, Opt. xvgr/xmgr file -px pullx.xvg Output, Opt. xvgr/xmgr file -pf pullf.xvg Output, Opt. xvgr/xmgr file -mtx nm.mtx Output, Opt. Hessian matrix -dn dipole.ndx Output, Opt. Index file Option Type Value Description -- -[no]h bool no Print help info and quit -niceint0 Set the nicelevel -deffnm string Set the default filename for all file options -[no]xvgrbool yes Add specific codes (legends etc.) in the output xvg files for the xmgrace program -[no]pd bool no Use particle decompostion -dd vector 0 0 0 Domain decomposition grid, 0 is optimize -npmeint-1 Number of separate nodes to be used for PME, -1 is guess -ddorder enum interleave DD node order: interleave, pp_pme or cartesian -[no]ddcheck bool yes Check for all bonded interactions with DD -rdd real 0 The maximum distance for bonded interactions with DD (nm), 0 is determine from initial coordinates -rconreal 0 Maximum distance for P-LINCS (nm), 0 is estimate -dlb enum autoDynamic load balancing (with DD): auto, no or yes -dds real 0.8 Minimum allowed dlb scaling of the DD cell size -[no]sum bool yes Sum the energies at every step -[no]v bool no Be loud and noisy -[no]compact bool yes Write a compact log file -[no]seppot bool no Write separate V and dVdl terms for each interaction type and node to the log file(s) -pforce real -1 Print all forces larger than this (kJ/mol nm) -[no]reprod bool no Try to avoid optimizations that affect binary reproducibility -cpt real 15 Checkpoint interval (minutes) -[no]append bool no Append to previous output files when restarting from checkpoint -maxhreal -1 Terminate after 0.99 times this time
[gmx-users] Distance Restraints Violations
Hi, all: Im using g_disre in gmx3.3.1 to calculate violations of distance restraints in a simulation and I saw the message: Fatal error: tpr inconsistency. ndr = 0, label = 1 The gmxdump of tpr shows functype[459]=DISRES, label= 1, type=1, low= 1.8007e-01, up1= 2.8001e-01, up2= 3.3013e-01, fac= 1.e+00) Im looking for hints in the gmx-users mail box and ... Usually problems here are related to the topology. Check whether one of the restraints is missing (typically the one with label = 362). This check is in g_disre only, not in mdrun or grompp. Maybe it should be in the latter... It seems that the restraint is there Am I forgeting something? Any hint will be sincerely appreciated! Im lost here! Francisco -- Francisco Gomes Neto Centro Nacional de Ressonancia Magnetica Nuclear - CNRMN Av. Brigadeiro Trompowisky, s/n - Predio CCS - Sala E-10 Rio de Janeiro - RJ - CEP 21.941-590 e-mail: [EMAIL PROTECTED] http://cnrmn.bioqmed.ufrj.br ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] distance restraints for a pdb file?
Dear All Is there any way of generating the distance restraints for a pdb file? Do any of the gromacs command support this problem or it has to be filled out manually? Best wishes Robert ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] distance restraints for a pdb file?
Robert Selwyne wrote: Dear All Is there any way of generating the distance restraints for a pdb file? Do any of the gromacs command support this problem or it has to be filled out manually? Best wishes Robert what do you mean generating the distance restraints? from nMR data? in that case there is a script in src/contrib/scripts ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- David. David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Distance restraints
zhong qiang wrote: Hi: I want to constuct my .top file, In my molecular system four calcium ions binding at four site, I use pdb2gmx make a top file, But there is not topology information about calcium ions, I insert a distance restraints in .top file, just like below: [ distance restraints ] ; aiaj type index type’ low up1 up2 fac 1460 207 1 2 1 0.0 0.3 0.4 1.0 1460 208 1 2 1 0.0 0.3 0.4 1.0 1460 210 1 2 1 0.0 0.3 0.4 1.0 1460 229 1 2 1 0.0 0.3 0.4 1.0 . then I run grompp -f fullmd_sol.mdp -c minimized_water.gro -p 1ckk.top -o fullmd.tpr But error message present: ERROR 1 [file 1ckk.top, line 9029]: Invalid directive distance restraints Then I delete line [ distance restraints ] !! That's a bit like a car mechanic telling you your car won't start because your battery is flat, and so you take it out and try again! the error report: Fatal error: Incorrect number of parameters - found 4, expected 3 or 6. Could somebody tell me how to add a distance restraints correctly? Yep. The first step will be to spell it like it is in the manual... distance_restraints Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] distance restraints: -merge
From: Owen, Michael [EMAIL PROTECTED] Reply-To: Discussion list for GROMACS users gmx-users@gromacs.org To: gmx-users@gromacs.org Subject: [gmx-users] distance restraints: -merge Date: Tue, 26 Sep 2006 11:10:15 -0500 Fellow gmx-users, I would like to constrain the distance of an ion to specific atoms of a protein. I recently read a message in which the use of the option -merge in the pdb2gmx program was suggested. How can I use this option to form these constraints? The -merge option is useful for merge two molecules. I assume that in your case the ion consists of just one atom. Then it is easier to just add this one atom by hand at the end of atoms of your protein and add the distance restraint. Berk. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] distance restraints: -merge
Title: distance restraints: -merge Fellow gmx-users, I would like to constrain the distance of an ion to specific atoms of a protein. I recently read a message in which the use of the option -merge in the pdb2gmx program was suggested. How can I use this option to form these constraints? Thank you for your assistance, Michael Owen ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Distance restraints
Title: Distance restraints Hello, I am trying to use NMR restraints to position a Cu2+ ion around specific residues of a peptide. I added Cu2+ using genion and then initiated grompp before an energy minim minimization. I received the following error message while executing grompp: --- Program grompp, VERSION 3.3.1 Source code file: toppush.c, line: 1108 Fatal error: [ file Ab_Cu.top, line 5864 ]: Atom index (67248) in distance_restraints out of bounds (1-1) --- Below is the entry in the topology file. Line 5864 contains the value 97 and the value 67248 refers is the atom number of the Cu2+ ion. [ distance_restraints ] ;ai aj type index type' low up1 up2 fac 67248 97 1 1 1 0.185 0.195 0.2 1.0 67248 196 1 1 1 0.185 0.195 0.2 1.0 67248 213 1 1 1 0.185 0.195 0.2 1.0 67248 148 1 1 1 0.195 0.205 0.21 1.0 Could you suggest any changes that would eliminate my error? Thanks in advance, Michael Owen ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] distance restraints problem
Dear All Im using distance restraints to force proper orientation of the ligand in the active site of the receptor protein (Im investigating different binding modes).I encountered a strange problem when defining distance restraints.I have protein and ligand topology combined in one itp file.At the end of this topology file (itp) I defined atoms pairs for distance restraints:.[ distance_restraints ]; ai aj type index type low up1 up2 fac 1384 4036 1 0 1 0.0 0.15 0.25 2.0 2957 4046 1 1 1 0.0 0.15 0.25 2.0 2957 4057 1 1 1 0.0 0.15 0.25 2.0 When looking at trajectory file I noticed that restraints are present but not between defined atoms but probably between pairs: 1383 40352956 40452956 4056 I checked the tpr file: gmxdump_mpi3 -s posre100.tpr and I found that position restraints are not between defined pairs but rather between (atom-1,atom-1).Dis. Rest.: nr: 9 multinr[division over processors]: 9 9 9 9 9 9 9 9 9 9 9 9 iatoms: 0 type=1244 (DISRES) 1383 4035 1 type=1245 (DISRES) 2956 4045 2 type=1245 (DISRES) 2956 4056 Numbering of atoms in my topology file is correct so I guess its not the case. What might be the problem. Am I doing something wrong. Im using gromacs3.3.Please give me comment on this and thank you for help. Best regardsMichal ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
