Hi Chris and Justin, On 18/08/2011, at 9:36 AM, Justin A. Lemkul wrote:
> > > chris.ne...@utoronto.ca wrote: >> You'll need to provide a much better report than this if you want to receive >> any useful help. >> Copy and paste the exact commands of what you did >> Copy and paste the exact log file and error messages > The command I had used (for both 4.0.7 and 4.5.4) are: pdb2gmx -f 1EXR.pdb -o 1EXR.gro -water spc -ignh -p 1EXR.top -i 1EXR.itp editconf -f 1EXR.gro -o 1EXR_box.gro -c -d 1.4 -bt cubic genbox -cp 1EXR_box.gro -cs spc216.gro -o 1EXR_solv.gro -p 1EXR.top -seed 5 grompp -f em.mdp -c 1EXR_solv.gro -p 1EXR.top -o ions.tpr genion -s ions.tpr -o 1EXR_solv_ions.gro -p 1EXR.top -pname NA+ -nname CL- -np 17 -seed 66 grompp -f em.mdp -c 1EXR_solv_ions.gro -p 1EXR.top -o em.tpr mpirun mdrun_d_mpi -v -s em.tpr -x 1EXR_em.xtc -e 1EXR_em.edr -g 1EXR_em.log -c 1EXR_em.gro grompp -f pr.mdp -c 1EXR_em.gro -p 1EXR.top -o pr.tpr mpirun mdrun_d_mpi -v -stepout 1000 -s pr.tpr -x 1EXR_pr.xtc -e 1EXR_pr.edr -g 1EXR_pr.log -o 1EXR_pr.trr -c 1EXR_pr.gro grompp -f md_start.mdp -c 1EXR_pr.gro -p 1EXR.top -o md.tpr mpirun mdrun_d_mpi -v -stepout 10000 -s md.tpr -x 1EXR_md.xtc -e 1EXR_md.edr -g 1EXR_md.log -o 1EXR_md.trr -c 1EXR_md.gro The em.mdp: integrator = steep maximum number of steps to integrate nsteps = 50000 ;Energy minimizing stuff emstep = 0.001 emtol = 100.0 ; OPTIONS FOR BONDS constraints = none ; OUTPUT CONTROL OPTIONS ; Output frequency for coords (x), velocities (v) and forces (f) nstxout = 1000 nstvout = 1000 nstfout = 1000 ; Output frequency and precision for xtc file nstxtcout = 1000 xtc-precision = 1000 ; Energy monitoring energygrps = system ; NEIGHBORSEARCHING PARAMETERS ; nblist update frequency nstlist = 5 ; ns algorithm (simple or grid) ns-type = Grid ; nblist cut-off rlist = 0.8 ; OPTIONS FOR ELECTROSTATICS AND VDW ; Method for doing electrostatics coulombtype = Reaction-Field rcoulomb = 1.4 ; Dielectric constant (DC) for cut-off or DC of reaction field epsilon-rf = 62 ; Method for doing Van der Waals vdw-type = Cut-off ; cut-off lengths rvdw = 1.4 ; Apply long range dispersion corrections for Energy and Pressure DispCorr = No ; Center of mass control nstcomm = 1000 ; Periodic boundary conditions pbc = xyz ; Mode for center of mass motion removal comm-mode = linear ; Groups for center of mass motion removal comm-grps = system the pr.mdp: define = -DPOSRES integrator = md dt = 0.002 ; ps ! nsteps = 50000 ; total 100ps. ; OPTIONS FOR BONDS ; Constrain control constraints = all-bonds ; Do not constrain the start configuration continuation = no ; Type of constraint algorithm constraint-algorithm = lincs ; OUTPUT CONTROL OPTIONS ; Output frequency for coords (x), velocities (v) and forces (f) nstxout = 100000 nstvout = 100000 nstfout = 100000 ; Output frequency and precision for xtc file nstxtcout = 5000 xtc-precision = 1000 ; Energy monitoring energygrps = Protein Non-protein nstenergy = 5000 ; NEIGHBORSEARCHING PARAMETERS ; nblist update frequency nstlist = 5 ; ns algorithm (simple or grid) ns-type = Grid ; nblist cut-off rlist = 0.8 ; OPTIONS FOR ELECTROSTATICS AND VDW ; Method for doing electrostatics coulombtype = Reaction-Field rcoulomb = 1.4 epsilon_rf = 62 ; As suggested at J Comput Chem. 2004 Oct;25(13):1656-76. vdw-type = Cut-off ; cut-off lengths rvdw = 1.4 ; Apply long range dispersion corrections for Energy and Pressure DispCorr = no ; OPTIONS FOR WEAK COUPLING ALGORITHMS ; Temperature coupling tcoupl = berendsen ; Groups to couple separately, time constant (ps) and reference temperature (K) tc-grps = Protein Non-Protein tau-t = 0.1 0.1 ref-t = 300 300 ; Pressure coupling Pcoupl = berendsen Pcoupltype = isotropic ; Time constant (ps), compressibility (1/bar) and reference P (bar) tau_p = 1.0 compressibility = 4.5e-5 ref_p = 1.0 ; Generate velocites is on at 290K - do not get velocity from gro file. gen_vel = yes gen_temp = 290 gen-seed = -1 ; Center of mass control nstcomm = 1000 ; Periodic boundary conditions pbc = xyz ; Mode for center of mass motion removal comm-mode = Linear ; Groups for center of mass motion removal comm-grps = system and the md.mdp: integrator = md dt = 0.002 ; ps ! nsteps = 2500000 ; total 5ns. ; OPTIONS FOR BONDS ; Constrain control constraints = all-bonds ; Do not constrain the start configuration continuation = no ; Type of constraint algorithm constraint-algorithm = lincs ; OUTPUT CONTROL OPTIONS ; Output frequency for coords (x), velocities (v) and forces (f) nstxout = 100000 nstvout = 100000 nstfout = 100000 ; Output frequency and precision for xtc file nstxtcout = 5000 xtc-precision = 1000 ; Energy monitoring energygrps = Protein Non-Protein nstenergy = 1000 ; NEIGHBORSEARCHING PARAMETERS ; nblist update frequency nstlist = 5 ; ns algorithm (simple or grid) ns-type = Grid ; nblist cut-off rlist = 0.8 ; OPTIONS FOR ELECTROSTATICS AND VDW ; Method for doing electrostatics coulombtype = Reaction-Field rcoulomb = 1.4 epsilon_rf = 62 ; As suggested at J Comput Chem. 2004 Oct;25(13):1656-76. vdw-type = Cut-off ; cut-off lengths rvdw = 1.4 ; Apply long range dispersion corrections for Energy and Pressure DispCorr = no ; OPTIONS FOR WEAK COUPLING ALGORITHMS ; Temperature coupling tcoupl = berendsen ; Groups to couple separately, time constant (ps) and reference temperature (K) tc-grps = Protein Non-Protein tau-t = 0.1 0.1 ref-t = 300 300 ; Pressure coupling Pcoupl = berendsen Pcoupltype = isotropic ; Time constant (ps), compressibility (1/bar) and reference P (bar) tau_p = 1.0 compressibility = 4.5e-5 ref_p = 1.0 ; Generate velocites is on at 290K - do not get velocity from gro file. gen_vel = yes gen_temp = 290 gen-seed = -1 ; Center of mass control nstcomm = 10000 ; Periodic boundary conditions pbc = xyz ; Mode for center of mass motion removal comm-mode = Linear ; Groups for center of mass motion removal comm-grps = system The error message we got are LINCS related, eg: Step 40941, time 40.941 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.000021, max 0.000112 (between atoms 981 and 982) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 981 982 34.0 0.0998 0.1000 0.1000 Step 40942, time 40.942 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.000140, max 0.001170 (between atoms 981 and 982) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 981 982 31.7 0.1000 0.1001 0.1000 Step 40943, time 40.943 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.000106, max 0.000860 (between atoms 981 and 982) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 981 982 30.2 0.1001 0.1001 0.1000 Step 40944, time 40.944 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.000053, max 0.000571 (between atoms 979 and 981) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 981 982 35.2 0.1001 0.1000 0.1000 Step 40945, time 40.945 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.000225, max 0.001915 (between atoms 981 and 982) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 981 982 36.4 0.1000 0.0998 0.1000 ------------------------------------------------------- Program mdrun_mpi_bg, VERSION 4.5.4 Source code file: ../../../gromacs-4.5.4/src/mdlib/constr.c, line: 176 Fatal error: Too many LINCS warnings (1000) If you know what you are doing you can adjust the lincs warning threshold in your mdp file or set the environment variable GMX_MAXCONSTRWARN to -1, but normally it is better to fix the problem For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors ------------------------------------------------------- Now, I think that there is some problem with gromacs 4.5.4 because the same system, using the same run parameter was successfully simulated using 4.0.7. I used GROMOS53a6 with SPC water whenever running this protein. The only difference between a crash and a successful run was gromacs version. > I'd also add that we need a detailed description of the system, including > force field used and any other special considerations (distance restraints, > modified parameters, etc). An .mdp file would also be useful for the run > that crashes. The only constraints I had in the system LINCS of all bonds. I didn't modified the FF in anyway. Best, Itamar > > -Justin > >> Do this for 4.0.7 and 4.5.4, for which I trust that you have been using >> exactly identical test systems. If not, then please try it again while >> conserving the system. >> Chris. >> -- original message -- >> Hi Matthew, >> Thanks for the reply. First, I don't thinks it is poorly compiled bin, as I >> used both GROMACS compiled by me (on my machine) or by the sys-admin on >> Linux cluster or blue-gene. >> The simulations using 4.5.4 crashed giving LINCS error, which is not the >> case with 4.0.7 (using the same mdp and pdb files). Second, I don't thinks >> it is poorly compiled bin, as I used both GROMACS compiled with me (on my >> machine) or by the sys-admin on Linux cluster/blue-gene. >> cheers, >> Itamar >> On 18 August 2011 01:48, Matthew Zwier <mczwier at gmail.com> wrote: >>> Could be a system blowing up, or perhaps a mis-compiled binary. What >>> error messages do you get when the crash occurs? >>> >>> On Tue, Aug 16, 2011 at 9:48 PM, Itamar Kass <itamar.kass at monash.edu> >>> wrote: >>> > Hi all GROMACS useres and developers, >>> > >>> > I am interesting in simulating a small protein (~140 aa) in water, with >>> and without Ca ions. In order to do so, I had used version 4.5.4. I had >>> solvate the protein in water, add ions to naturalise the systems, >>> equilibrated the systems and then tried productive runs. Now, no matter what >>> I did, it crashed after few ps's of free MD or during the PR runs. >>> > >>> > Few of the things I had tried are: >>> > 1. Running the simulations on different systems (OSX, linux or >>> blue-gene). >>> > 2. Using single or double precision versions. >>> > 3. An equilibration stage, 1ns long with a time-step of 1fs, during which >>> the restrained forces where gradually reduced from 1000 to 50 kJ mol-1 nm-2. >>> > 4. Running part of the equilibration stage as NVT and then switched to >>> NPT. >>> > 5. Started from different x-ray structures, with resolutions differ from >>> 2.5 to 1.7 Angstrom. >>> > >>> > Finally I had moved back to 4.0.7 which worked like charm. I wonder if >>> someone else had encounter something like this. Attached please find the mdp >>> files I used. >>> > >>> > All the best, >>> > Itamar. >>> > >>> > >>> > >>> > > > -- > ======================================== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > ======================================== > -- > gmx-users mailing list gmx-users@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 ----- "In theory, there is no difference between theory and practice. But, in practice, there is." - Jan L.A. van de Snepscheut =========================================== | Itamar Kass, Ph.D. | Postdoctoral Research Fellow | | Department of Biochemistry and Molecular Biology | Building 77 Clayton Campus | Wellington Road | Monash University, | Victoria 3800 | Australia | | Tel: +61 3 9902 9376 | Fax: +61 3 9902 9500 | E-mail: itamar.k...@monash.edu ============================================
-- gmx-users mailing list gmx-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