Hi Justin, THanks for the input. So I traced back to my energy minimization steps, and am getting the error message after I execute the following line:
$mdrun -s 1JFF_em.tpr -o 1JFF_em.trr -c 1JFF_b4pr.gro -e em.edr output: Back Off! I just backed up md.log to ./#md.log.2# Reading file 1JFF_em.tpr, VERSION 4.5.3 (single precision) Starting 24 threads Will use 15 particle-particle and 9 PME only nodes This is a guess, check the performance at the end of the log file ------------------------------------------------------- Program mdrun, VERSION 4.5.3 Source code file: domdec.c, line: 6428 Fatal error: There is no domain decomposition for 15 nodes that is compatible with the given box and a minimum cell size of 2.92429 nm Change the number of nodes or mdrun option -rdd Look in the log file for details on the domain decomposition For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors ------------------------------------------------------- I figure the problem must lie within my em.mdp file: title = 1JFF cpp = /lib/cpp ; location of cpp on SGI define = -DFLEX_SPC ; Use Ferguson’s Flexible water model [4] constraints = none integrator = steep dt = 0.001 ; ps ! nsteps = 10000 nstlist = 10 ns_type = grid rlist = 0.9 coulombtype = PME ; Use particle-mesh ewald rcoulomb = 0.9 rvdw = 1.0 fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 4 ewald_rtol = 1e-5 optimize_fft = yes ; ; Energy minimizing stuff ; emtol = 1000.0 emstep = 0.01 ~ I figure this is an issue related to with PME and the Fourier spacing? Thanks, rainy908 On 17 August 2011 17:55, Justin A. Lemkul <jalem...@vt.edu> wrote: rainy908 wrote: Dear gmx-users: Thanks Justin for your help. But now I am experiencing a Segmentation fault error when executing mdrun. I've perused the archives but found none of the threads on segmentation faults similar to my case here. I believe the segmentation fault is caused by the awkward positioning of atoms 8443 and 8446 with respect to one another, but am not 100%. Any advice would be especially welcome. My files are as follows: md.mdp ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ title = 1JFF MD cpp = /lib/cpp ; location of cpp on SGI constraints = all-bonds integrator = md dt = 0.0001 ; ps nsteps = 25000 ; nstcomm = 1 nstxout = 500 ; output coordinates every 1.0 ps nstvout = 0 nstfout = 0 nstlist = 10 ns_type = grid rlist = 0.9 coulombtype = PME rcoulomb = 0.9 rvdw = 1.0 fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 6 ewald_rtol = 1e-5 optimize_fft = yes ; Berendsen temperature coupling is on in four groups Tcoupl = berendsen tau_t = 0.1 tc-grps = system ref_t = 310 ; Pressure coupling is on Pcoupl = berendsen pcoupltype = isotropic tau_p = 0.5 compressibility = 4.5e-5 ref_p = 1.0 ; Generate velocites is on at 310 K. gen_vel = yes gen_temp = 310.0 gen_seed = 173529 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ error output file: ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .. .. Back Off! I just backed up md.log to ./#md.log.1# Getting Loaded... Reading file 1JFF_md.tpr, VERSION 4.5.3 (single precision) Starting 8 threads Loaded with Money Making 3D domain decomposition 2 x 2 x 2 Back Off! I just backed up 1JFF_md.trr to ./#1JFF_md.trr.1# Back Off! I just backed up 1JFF_md.edr to ./#1JFF_md.edr.1# Step 0, time 0 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.046849, max 1.014038 (between atoms 8541 and 8539) Step 0, time 0 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.001453, max 0.034820 (between atoms 315 and 317) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length If mdrun is failing at step 0, it indicates that your system is physically unreasonable. Either the starting configuration has atomic clashes that have not been resolved (and thus you need better EM and/or equilibration) or that the parameters assigned to the molecules in your system are unreasonable. -Justin Step 0, time 0 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.048739, max 1.100685 (between atoms 8422 and 8421) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length .. .. <snip> .. .. starting mdrun 'TUBULIN ALPHA CHAIN' 25000 steps, 50.0 ps. Warning: 1-4 interaction between 8443 and 8446 at distance 2.853 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 .. .. <snip> .. .. step 0: Water molecule starting at atom 23781 can not be settled. Check for bad contacts and/or reduce the timestep if appropriate. Back Off! I just backed up step0b_n0.pdb to ./#step0b_n0.pdb.1# Back Off! I just backed up step0b_n1.pdb to ./#step0b_n1.pdb.1# Back Off! I just backed up step0b_n5.pdb to ./#step0b_n5.pdb.2# Back Off! I just backed up step0b_n3.pdb to ./#step0b_n3.pdb.2# Back Off! I just backed up step0c_n0.pdb to ./#step0c_n0.pdb.1# Back Off! I just backed up step0c_n1.pdb to ./#step0c_n1.pdb.1# Back Off! I just backed up step0c_n5.pdb to ./#step0c_n5.pdb.2# Back Off! I just backed up step0c_n3.pdb to ./#step0c_n3.pdb.2# Wrote pdb files with previous and current coordinates Wrote pdb files with previous and current coordinates Wrote pdb files with previous and current coordinates Wrote pdb files with previous and current coordinates Wrote pdb files with previous and current coordinates ^Mstep 0/opt/sge/jacobson/spool/node-2-05/job_scripts/1097116: line 21: 1473 Segmentation fault (core dumped) $MDRUN -machinefile $TMPDIR/machines -np $NSLOTS $MDRUN -v -nice 0 -np $NSLOTS -s 1JFF_md.tpr -o 1JFF_md.trr -c 1JFF_pmd.gro -x 1JFF_md.xtc -e 1JFF_md.edr On 16 August 2011 10:58, Justin A. Lemkul <jalem...@vt.edu> wrote: rainy908 wrote: Hi, I get the error "Atomtype CR1 not found" when I execute grompp. After perusing the gmx archives, I understand this error has to do with the lack of "CR1" being specified in the force field. However, I did include the appropriate .itp files in my .top file (shown below). As you can see, obviously CR1 is specified in taxol.itp and gtp.itp. Therefore, I'm not sure what exactly is the problem here. You're mixing and matching force fields. PRODRG produces Gromos-compatible parameters (and does a poor job of that - I can tell you now that the charges assigned to the aromatic C and H of taxol are total junk). You're then trying to combine these parameters with OPLS. Even if you could somehow hack the topology together, the results would be useless. For more about the hazards of PRODRG, see http://pubs.acs.org/doi/abs/10.1021/ci100335w. The solution is to pick a force field and apply it uniformly to the system you're working with. -Justin Any input on this issue would be greatly appreciated. 1JFF.top ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ; File '1JFF.top' was generated ; By user: onbekend (0) ; On host: onbekend ; At date: Mon Aug 15 17:22:01 2011 ; ; This is a standalone topology file ; ; It was generated using program: ; pdb2gmx - VERSION 4.5.3 ; ; Command line was: ; /software/gromacs/gromacs-4.5.3-x86_64/bin/pdb2gmx -f 1JFF_new.pdb -o 1JFF.gro -p 1JFF.top ; ; Force field was read from the standard Gromacs share directory. ; ; Include forcefield parameters #include "oplsaa.ff/forcefield.itp" #include "taxol.itp" #include "gdp.itp" #include "gtp.itp" ; Include chain topologies #include "1JFF_Protein_chain_A.itp" #include "1JFF_Protein_chain_B.itp" #include "1JFF_Ion_chain_A2.itp" ; Include water topology #include "oplsaa.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 "oplsaa.ff/ions.itp" [ system ] ; Name TUBULIN ALPHA CHAIN; TUBULIN BETA CHAIN in water [ molecules ] ; Compound #mols Protein_chain_A 1 Protein_chain_B 1 Ion_chain_A2 1 Taxol 1 GDP 1 GTP 1 SOL 21016 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ taxol.itp ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ; This file was generated by PRODRG version AA081006.0504 ; PRODRG written/copyrighted by Daan van Aalten ; and Alexander Schuettelkopf ; ; Questions/comments to d...@davapc1.bioch.dundee.ac.uk ; ; When using this software in a publication, cite: ; A. W. Schuettelkopf and D. M. F. van Aalten (2004). ; PRODRG - a tool for high-throughput crystallography ; of protein-ligand complexes. ; Acta Crystallogr. D60, 1355--1363. ; ; [ moleculetype ] ; Name nrexcl TA1 3 [ atoms ] ; nr type resnr resid atom cgnr charge mass 1 CR1 1 TA1 C05 1 -0.015 12.0110 2 HC 1 TA1 H05 1 0.015 1.0080 3 CR1 1 TA1 C06 2 -0.012 12.0110 4 HC 1 TA1 H06 2 0.019 1.0080 5 CR1 1 TA1 C07 2 -0.012 12.0110 6 HC 1 TA1 H07 2 0.019 1.0080 7 CR1 1 TA1 C08 2 -0.012 12.0110 8 HC 1 TA1 H08 2 0.019 1.0080 9 CR1 1 TA1 C09 2 -0.012 12.0110 10 HC 1 TA1 H09 2 0.019 1.0080 11 C 1 TA1 C04 2 -0.028 12.0110 12 C 1 TA1 C03 3 0.357 12.0110 13 O 1 TA1 O03 3 -0.710 15.9994 14 OA 1 TA1 O02 3 -0.186 15.9994 15 CH1 1 TA1 C02 3 0.235 13.0190 16 CH1 1 TA1 C10 3 0.148 13.0190 17 CH1 1 TA1 C11 3 0.156 12.0110 18 OA 1 TA1 O04 4 -0.175 15.9994 19 C 1 TA1 C12 4 0.378 12.0110 20 O 1 TA1 O05 4 -0.670 15.9994 ... ... <snip> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gtp.itp ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ moleculetype ] ; Name nrexcl GTP 3 [ atoms ] ; nr type resnr resid atom cgnr charge mass 1 O 1 GTP O6 1 -0.266 15.9994 2 C 1 GTP C6 1 0.216 12.0110 3 NR 1 GTP N1 1 -0.008 14.0067 4 H 1 GTP H1 1 -0.020 1.0080 5 C 1 GTP C2 1 0.322 12.0110 6 NT 1 GTP N2 1 -0.001 14.0067 7 H 1 GTP H22 1 -0.020 1.0080 8 H 1 GTP H21 1 -0.020 1.0080 9 NR 1 GTP N3 1 -0.203 14.0067 10 C 1 GTP C4 2 0.133 12.0110 11 C 1 GTP C5 2 0.048 12.0110 12 NR 1 GTP N7 2 -0.321 14.0067 13 CR1 1 GTP C8 2 -0.037 12.0110 14 HC 1 GTP H8 2 -0.019 1.0080 15 NR 1 GTP N9 2 0.112 14.0067 16 CH1 1 GTP CAU 2 0.084 13.0190 .. .. <snip> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -- ======================================== 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 ======================================== -- ======================================== 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