> Robert Fenwick wrote: >> Hi, >> >> I wanted to run one of the gromacs 4.0 benchmarks on a new cluster >> that we have and also wanted to see the affect of this 4 fs time step. >> If it would not be too much trouble would it be possible for the >> setups of either the PLINCS paper or the GROMACS 4.0 paper to be >> placed somewhere on the website. Specifically I am intersted in the >> lysozyme benchmark, however I suspect others might like the membrane >> system to as well. >> >> I have tried to set a similar simulation up, but it is not able to run >> with 4 fs integration. >> > > So what exactly is going wrong? What is in your .mdp file? It is probably > better for you to post this information here and receive feedback, so that > others can make use of it later.
I've followed what I think is a sensible setup, which comes from the GROMACS workshop pre-workshop tutorial. Comments are wellcome, I generate this using a bash script for convenience: grep -v HOH original/1LYD.pdb > ./prot1LYD.pdb pdb2gmx -f prot1LYD.pdb -ter -ignh -vsite hydrogens -water tip3p select OPLS, 0, 0 editconf -f conf.gro -bt dodecahedron -d 0.7 -o box.gro genbox -cp box.gro -cs spc216.gro -p topol.top -o solvated.gro grompp -f em.mdp -p topol.top -c solvated.gro -o sol.tpr genion -s sol.tpr -nn 8 -nname CL- -nq -1 -np 0 -pname NA+ -pq 1 -p topol.top -o solvatedIon.gro select 12 (SOL) grompp -f em.mdp -p topol.top -c solvatedIon.gro -o em.tpr mdrun -v -deffnm em grompp -f pr.mdp -p topol.top -c em.gro -o pr.tpr mpirun -np 16 mdrun_mpi -v -deffnm pr -npme 8 grompp -f run.mdp -p topol.top -c pr.gro -o run.tpr mpirun -np 16 mdrun_mpi -v -deffnm run -npme 8 The inputs are, and come directly from the article Hess et al., 2008 JCTC GROMACS 4 : :::::::::::::: em.mdp :::::::::::::: integrator = steep nsteps = 200 nstlist = 10 rlist = 1.0 coulombtype = pme fourierspacing = 0.125 rcoulomb = 1.0 vdw-type = cut-off rvdw = 1.0 lincs-order = 6 nstenergy = 10 :::::::::::::: pr.mdp :::::::::::::: integrator = md nsteps = 50000 dt = 0.002 nstlist = 10 rlist = 1.0 coulombtype = pme fourierspacing = 0.125 rcoulomb = 1.0 vdw-type = cut-off rvdw = 1.0 lincs-order = 6 tcoupl = Berendsen tc-grps = protein non-protein tau-t = 0.1 0.1 ref-t = 298 298 Pcoupl = Berendsen tau-p = 1.0 compressibility = 1e-5 1e-5 1e-5 0 0 0 ref-p = 1.0 nstenergy = 100 define = -DPOSRES :::::::::::::: run.mdp :::::::::::::: integrator = md nsteps = 50000 dt = 0.004 nstlist = 5 rlist = 1.0 coulombtype = pme fourierspacing = 0.125 rcoulomb = 1.0 vdw-type = cut-off rvdw = 1.0 lincs-order = 6 tcoupl = Berendsen tc-grps = protein non-protein tau-t = 0.1 0.1 ref-t = 298 298 nstxout = 1000 nstvout = 1000 nstxtcout = 100 nstenergy = 100 The simulation dies with: Step 6, time 0.024 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.222533, max 1.229818 (between atoms 328 and 329) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 1970 1973 90.0 0.2413 0.3543 0.1930 1888 1891 65.8 0.4413 0.1879 0.1930 447 449 59.2 0.2406 0.1939 0.1939 656 660 90.0 0.1930 0.4267 0.1930 616 619 90.0 0.1924 0.2612 0.1930 477 480 89.9 0.2945 0.3802 0.1930 319 329 65.3 0.1670 0.1816 0.1670 328 329 90.0 0.0915 0.2039 0.0915 762 765 42.4 0.1584 0.1554 0.1583 762 766 44.0 0.1581 0.1616 0.1583 t = 0.024 ps: Water molecule starting at atom 16419 can not be settled. Check for bad contacts and/or reduce the timestep. Wrote pdb files with previous and current coordinates Warning: 1-4 interaction between 949 and 963 at distance 6.212 which is larger than the 1-4 table size 2.000 nm These are ignored for the rest of the simulation This usually means your system is exploding, if not, you should increase table-extension in your mdp file or with user tables increase the table size Warning: 1-4 interaction between 747 and 753 at distance 14.118 which is larger than the 1-4 table size 2.000 nm These are ignored for the rest of the simulation This usually means your system is exploding, if not, you should increase table-extension in your mdp file or with user tables increase the table size ------------------------------------------------------- Program mdrun_mpi, VERSION 4.0.3 Source code file: pme.c, line: 518 Fatal error: 11 particles communicated to PME node 3 are more than a cell length out of the domain decomposition cell of their charge group ------------------------------------------------------- > The methodology for the lysozyme benchmark is pretty explicit in the Gromacs 4 > paper; is there some aspect that is not clear? I agree that the paper is clear, I ask because it is obvious that I am doing something wrong the system should be stable! > -Justin > >> >> Bryn >> _______________________________________________ >> gmx-users mailing list gmx-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 >> > > -- > ======================================== > > Justin A. Lemkul > Graduate Research Assistant > 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://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