Re: [gmx-users] Issue running gromacs in Cluster
On 5/13/13 4:44 AM, Sainitin Donakonda wrote: Thank you very much for inputs but i forgot to mention in previous query i got one error ..with other protein ligand simulation i used same MD file saving 200 steps.. *Cannot write trajectory frame; maybe you are out of quota?* * * Whats the solution for this error ? is this same problem with saving 200 steps? or some thing else You already got an answer to this - you're saving full-precision output far too often. The sysadmins of clusters typically put in place quotas (limits) on how much disk space any one user can occupy, to prevent one person from sucking up all the available resources. Or, if you're running on a local workstation or small cluster, you're just filling up your hard disk. Just because it "worked" before doesn't mean it will again - you have run out of available room to write data. Consider whether you need full-precision output every 0.4 ps - the answer is almost certainly "no." -Justin On Mon, May 13, 2013 at 10:25 AM, Broadbent, Richard < richard.broadben...@imperial.ac.uk> wrote: On 13/05/2013 08:46, "Sainitin Donakonda" wrote: Hello, I am trying to run 20 ns protein ligand simulation on cluster using following MD.MDP file ; 7.3.3 Run Control integrator = md; leap-frog integrator dt = 0.002 ; 2 fs nsteps = 500; maximum number of steps to integrate ; 7.3.8 Output Control nstxout = 200 ; suppress .trr output nstvout = 200; suppress .trr output This writes out every 0.4 ps I doubt that¹s what you want nstenergy = 1000 ; save energies every 2 ps nstlog = 1000 ; update log file every 2 ps nstxtcout = 1000 ; write .xtc trajectory every 2 ps energygrps = Protein LIG ; 7.3.9 Neighbor Searching nstlist = 5 ; [steps] freq to update neighbor list ns_type = grid ; method of updating neighbor list pbc = xyz ; periodic boundary conditions in all directions rlist = 1.2 ; [nm] cut-off distance for the short-range neighbor list ; 7.3.10 Electrostatics coulombtype = PME ; Particle-Mesh Ewald electrostatics rcoulomb= 1.2 ; [nm] distance for Coulomb cut-off ; 7.3.11 VdW vdwtype = switch ; twin-range cut-off with rlist where rvdw >= rlist rvdw= 1.2 ; [nm] distance for LJ cut-off rvdw_switch = 0.8 ; Start switching th LJ potential 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 Berendsen-thermostat tc_grps = Protein_LIG Water_and_ions; groups to couple seperately to temperature bath tau_t = 0.10.1; [ps] time constant for coupling ref_t = 300300; [K] reference temperature for coupling ; Pressure coupling pcoupl = Parrinello-Rahman ; pressure coupling is on for NPT pcoupltype = isotropic ; uniform scaling of box vectors tau_p = 2.0 ; time constant, in ps ref_p = 1.0 ; reference pressure, in bar compressibility = 4.5e-5; isothermal compressibility of water, bar^-1 refcoord_scaling= com ; 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 *and im using following commands dividing 20 ns to 10 ns each via extending simulation* *#This is the first simulation MD.mdp file contains 20 ns setup* grompp -f MD.mdp -c npt.gro -t npt.cpt -p topol.top -n index.ndx -o MD_first10.tpr mpirun -n 16 mdrun -s MD_first10.tpr -deffnm MD_first10 -np 16 *#This extends 10 ns simulation* tpbconv -s MD_first10.tpr -extend 1 -o md_extended.tpr mpirun -n 16 mdrun -s md_extended.tpr -deff
Re: [gmx-users] Issue running gromacs in Cluster
Thank you very much for inputs but i forgot to mention in previous query i got one error ..with other protein ligand simulation i used same MD file saving 200 steps.. *Cannot write trajectory frame; maybe you are out of quota?* * * Whats the solution for this error ? is this same problem with saving 200 steps? or some thing else Thanks, Sainitin On Mon, May 13, 2013 at 10:25 AM, Broadbent, Richard < richard.broadben...@imperial.ac.uk> wrote: > > > On 13/05/2013 08:46, "Sainitin Donakonda" wrote: > > >Hello, > > > >I am trying to run 20 ns protein ligand simulation on cluster using > >following MD.MDP file > > > >; 7.3.3 Run Control > >integrator = md; leap-frog integrator > >dt = 0.002 ; 2 fs > >nsteps = 500; maximum number of steps > >to integrate > > > > > > > >; 7.3.8 Output Control > >nstxout = 200 ; suppress .trr output > >nstvout = 200; suppress .trr output > > This writes out every 0.4 ps I doubt that¹s what you want > > >nstenergy = 1000 ; save energies every 2 ps > >nstlog = 1000 ; update log file every 2 ps > >nstxtcout = 1000 ; write .xtc trajectory every 2 ps > >energygrps = Protein LIG > > > >; 7.3.9 Neighbor Searching > >nstlist = 5 ; [steps] freq to update neighbor > >list > >ns_type = grid ; method of updating neighbor list > >pbc = xyz ; periodic boundary conditions in > >all directions > >rlist = 1.2 ; [nm] cut-off distance for the > >short-range neighbor list > > > >; 7.3.10 Electrostatics > >coulombtype = PME ; Particle-Mesh Ewald > >electrostatics > >rcoulomb= 1.2 ; [nm] distance for Coulomb > >cut-off > > > >; 7.3.11 VdW > >vdwtype = switch ; twin-range cut-off with rlist > >where rvdw >= rlist > >rvdw= 1.2 ; [nm] distance for LJ cut-off > >rvdw_switch = 0.8 ; Start switching th LJ potential > >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 Berendsen-thermostat > >tc_grps = Protein_LIG Water_and_ions; groups to couple > >seperately to temperature bath > >tau_t = 0.10.1; [ps] time > >constant for coupling > >ref_t = 300300; [K] reference > >temperature for coupling > > > >; Pressure coupling > >pcoupl = Parrinello-Rahman ; pressure coupling is on for > >NPT > >pcoupltype = isotropic ; uniform scaling of box > >vectors > >tau_p = 2.0 ; time constant, in ps > >ref_p = 1.0 ; reference pressure, in bar > >compressibility = 4.5e-5; isothermal compressibility > >of > >water, bar^-1 > >refcoord_scaling= com > > > >; 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 > > > > > >*and im using following commands dividing 20 ns to 10 ns each via > >extending > >simulation* > > > > > >*#This is the first simulation MD.mdp file contains 20 ns setup* > >grompp -f MD.mdp -c npt.gro -t npt.cpt -p topol.top -n index.ndx -o > >MD_first10.tpr > > > >mpirun -n 16 mdrun -s MD_first10.tpr -deffnm MD_first10 -np 16 > > > >*#This extends 10 ns simulation* > >tpbconv -s MD_first10.tpr -extend 1 -o md_extended.tpr > > > >mpirun -n 16 mdrun -s md_extended.tpr -deffnm MD_first10 -cpi > >MD_first10.cpt -append -np 16 > > > > > >But it is crashed giving following error > > > >*XTC error - maybe you are out of quota?* > >* > >* > >*dont know why it happened it is because as im saving .trr file every > >200ps? is it creating large files? or should i give different name in > >e
Re: [gmx-users] Issue running gromacs in Cluster
On 13/05/2013 08:46, "Sainitin Donakonda" wrote: >Hello, > >I am trying to run 20 ns protein ligand simulation on cluster using >following MD.MDP file > >; 7.3.3 Run Control >integrator = md; leap-frog integrator >dt = 0.002 ; 2 fs >nsteps = 500; maximum number of steps >to integrate > > > >; 7.3.8 Output Control >nstxout = 200 ; suppress .trr output >nstvout = 200; suppress .trr output This writes out every 0.4 ps I doubt that¹s what you want >nstenergy = 1000 ; save energies every 2 ps >nstlog = 1000 ; update log file every 2 ps >nstxtcout = 1000 ; write .xtc trajectory every 2 ps >energygrps = Protein LIG > >; 7.3.9 Neighbor Searching >nstlist = 5 ; [steps] freq to update neighbor >list >ns_type = grid ; method of updating neighbor list >pbc = xyz ; periodic boundary conditions in >all directions >rlist = 1.2 ; [nm] cut-off distance for the >short-range neighbor list > >; 7.3.10 Electrostatics >coulombtype = PME ; Particle-Mesh Ewald >electrostatics >rcoulomb= 1.2 ; [nm] distance for Coulomb >cut-off > >; 7.3.11 VdW >vdwtype = switch ; twin-range cut-off with rlist >where rvdw >= rlist >rvdw= 1.2 ; [nm] distance for LJ cut-off >rvdw_switch = 0.8 ; Start switching th LJ potential >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 Berendsen-thermostat >tc_grps = Protein_LIG Water_and_ions; groups to couple >seperately to temperature bath >tau_t = 0.10.1; [ps] time >constant for coupling >ref_t = 300300; [K] reference >temperature for coupling > >; Pressure coupling >pcoupl = Parrinello-Rahman ; pressure coupling is on for >NPT >pcoupltype = isotropic ; uniform scaling of box >vectors >tau_p = 2.0 ; time constant, in ps >ref_p = 1.0 ; reference pressure, in bar >compressibility = 4.5e-5; isothermal compressibility >of >water, bar^-1 >refcoord_scaling= com > >; 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 > > >*and im using following commands dividing 20 ns to 10 ns each via >extending >simulation* > > >*#This is the first simulation MD.mdp file contains 20 ns setup* >grompp -f MD.mdp -c npt.gro -t npt.cpt -p topol.top -n index.ndx -o >MD_first10.tpr > >mpirun -n 16 mdrun -s MD_first10.tpr -deffnm MD_first10 -np 16 > >*#This extends 10 ns simulation* >tpbconv -s MD_first10.tpr -extend 1 -o md_extended.tpr > >mpirun -n 16 mdrun -s md_extended.tpr -deffnm MD_first10 -cpi >MD_first10.cpt -append -np 16 > > >But it is crashed giving following error > >*XTC error - maybe you are out of quota?* >* >* >*dont know why it happened it is because as im saving .trr file every >200ps? is it creating large files? or should i give different name in >extending simulation?* No you are writing every 200 steps not ps this is explained in the turtorials and the manual You can check the file size by looking at ls -lh my guess is both the trr and xtc will be gigantic >* >* >*Please help* >* >* >*Thanks,* >*Nitin* >-- >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
Re: [gmx-users] Issue running gromacs in Cluster
You may have created large files and thus got out of quota on the disc. Check your quota and consider reducing the frequency of saving coordinates. On May 13, 2013, at 9:46, Sainitin Donakonda wrote: > Hello, > > I am trying to run 20 ns protein ligand simulation on cluster using > following MD.MDP file > > ; 7.3.3 Run Control > integrator = md; leap-frog integrator > dt = 0.002 ; 2 fs > nsteps = 500; maximum number of steps > to integrate > > > > ; 7.3.8 Output Control > nstxout = 200 ; suppress .trr output > nstvout = 200; suppress .trr output > nstenergy = 1000 ; save energies every 2 ps > nstlog = 1000 ; update log file every 2 ps > nstxtcout = 1000 ; write .xtc trajectory every 2 ps > energygrps = Protein LIG > > ; 7.3.9 Neighbor Searching > nstlist = 5 ; [steps] freq to update neighbor > list > ns_type = grid ; method of updating neighbor list > pbc = xyz ; periodic boundary conditions in > all directions > rlist = 1.2 ; [nm] cut-off distance for the > short-range neighbor list > > ; 7.3.10 Electrostatics > coulombtype = PME ; Particle-Mesh Ewald electrostatics > rcoulomb= 1.2 ; [nm] distance for Coulomb cut-off > > ; 7.3.11 VdW > vdwtype = switch ; twin-range cut-off with rlist > where rvdw >= rlist > rvdw= 1.2 ; [nm] distance for LJ cut-off > rvdw_switch = 0.8 ; Start switching th LJ potential > 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 Berendsen-thermostat > tc_grps = Protein_LIG Water_and_ions; groups to couple > seperately to temperature bath > tau_t = 0.10.1; [ps] time > constant for coupling > ref_t = 300300; [K] reference > temperature for coupling > > ; Pressure coupling > pcoupl = Parrinello-Rahman ; pressure coupling is on for > NPT > pcoupltype = isotropic ; uniform scaling of box vectors > tau_p = 2.0 ; time constant, in ps > ref_p = 1.0 ; reference pressure, in bar > compressibility = 4.5e-5; isothermal compressibility of > water, bar^-1 > refcoord_scaling= com > > ; 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 > > > *and im using following commands dividing 20 ns to 10 ns each via extending > simulation* > > > *#This is the first simulation MD.mdp file contains 20 ns setup* > grompp -f MD.mdp -c npt.gro -t npt.cpt -p topol.top -n index.ndx -o > MD_first10.tpr > > mpirun -n 16 mdrun -s MD_first10.tpr -deffnm MD_first10 -np 16 > > *#This extends 10 ns simulation* > tpbconv -s MD_first10.tpr -extend 1 -o md_extended.tpr > > mpirun -n 16 mdrun -s md_extended.tpr -deffnm MD_first10 -cpi > MD_first10.cpt -append -np 16 > > > But it is crashed giving following error > > *XTC error - maybe you are out of quota?* > * > * > *dont know why it happened it is because as im saving .trr file every > 200ps? is it creating large files? or should i give different name in > extending simulation?* > * > * > *Please help* > * > * > *Thanks,* > *Nitin* > -- > 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-user
[gmx-users] Issue running gromacs in Cluster
Hello, I am trying to run 20 ns protein ligand simulation on cluster using following MD.MDP file ; 7.3.3 Run Control integrator = md; leap-frog integrator dt = 0.002 ; 2 fs nsteps = 500; maximum number of steps to integrate ; 7.3.8 Output Control nstxout = 200 ; suppress .trr output nstvout = 200; suppress .trr output nstenergy = 1000 ; save energies every 2 ps nstlog = 1000 ; update log file every 2 ps nstxtcout = 1000 ; write .xtc trajectory every 2 ps energygrps = Protein LIG ; 7.3.9 Neighbor Searching nstlist = 5 ; [steps] freq to update neighbor list ns_type = grid ; method of updating neighbor list pbc = xyz ; periodic boundary conditions in all directions rlist = 1.2 ; [nm] cut-off distance for the short-range neighbor list ; 7.3.10 Electrostatics coulombtype = PME ; Particle-Mesh Ewald electrostatics rcoulomb= 1.2 ; [nm] distance for Coulomb cut-off ; 7.3.11 VdW vdwtype = switch ; twin-range cut-off with rlist where rvdw >= rlist rvdw= 1.2 ; [nm] distance for LJ cut-off rvdw_switch = 0.8 ; Start switching th LJ potential 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 Berendsen-thermostat tc_grps = Protein_LIG Water_and_ions; groups to couple seperately to temperature bath tau_t = 0.10.1; [ps] time constant for coupling ref_t = 300300; [K] reference temperature for coupling ; Pressure coupling pcoupl = Parrinello-Rahman ; pressure coupling is on for NPT pcoupltype = isotropic ; uniform scaling of box vectors tau_p = 2.0 ; time constant, in ps ref_p = 1.0 ; reference pressure, in bar compressibility = 4.5e-5; isothermal compressibility of water, bar^-1 refcoord_scaling= com ; 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 *and im using following commands dividing 20 ns to 10 ns each via extending simulation* *#This is the first simulation MD.mdp file contains 20 ns setup* grompp -f MD.mdp -c npt.gro -t npt.cpt -p topol.top -n index.ndx -o MD_first10.tpr mpirun -n 16 mdrun -s MD_first10.tpr -deffnm MD_first10 -np 16 *#This extends 10 ns simulation* tpbconv -s MD_first10.tpr -extend 1 -o md_extended.tpr mpirun -n 16 mdrun -s md_extended.tpr -deffnm MD_first10 -cpi MD_first10.cpt -append -np 16 But it is crashed giving following error *XTC error - maybe you are out of quota?* * * *dont know why it happened it is because as im saving .trr file every 200ps? is it creating large files? or should i give different name in extending simulation?* * * *Please help* * * *Thanks,* *Nitin* -- 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
