Hi gromacs users, I apologize in advance for the long mail, but I have been having some trouble with my gromacs simulations lately.
My system consists of two popypeptide chains and a small ligand (or drug like compound). I obtain the required gromacs topologies for the ligand/drug from PRODRG dundee server. The steps I use for a MD simulation using gromacs is briefly as follows: 1) get ligand file with required polar hydrogens and gromacs ligand .itp file from prodrg server 2) run pdb2gmx using the gmx force field and spce water 3) correctly update the protein topology file to include ligand itp file header, number of ligand molecules and also make sure the output file from pdb2gmx contains the necessary ligand coordinates 3) set up box around this system, fill box with solvent (water), neutralize system using genion 4) set up files to run energy minimization on system, run energy minimization 5) set up files to run position restrained dynamics and run position restrained dynamics 6) setup up files and run Molecular dynamics on the system for ~ 10 ps The above set up worked with one of the protease-ligand complex I was testing, but had been failing for another viral protease. The errors vary depending on the run, and in some simulations, I get an error during the Energy minimization step: (section of em log file pasted below) ------------------------------------------------------------ Enabling SPC water optimization for 41607 molecules. Will do PME sum in reciprocal space. ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ U. Essman, L. Perela, M. L. Berkowitz, T. Darden, H. Lee and L. G. Pedersen A smooth particle mesh Ewald method J. Chem. Phys. 103 (1995) pp. 8577-8592 -------- -------- --- Thank You --- -------- -------- Removing pbc first time Done rmpbc Initiating Steepest Descents Center of mass motion removal mode is Linear We have the following groups for center of mass motion removal: 0: rest, initial mass: 129215 Started Steepest Descents on node 0 Wed Dec 19 10:33:25 2007 ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ S. Miyamoto and P. A. Kollman SETTLE: An Analytical Version of the SHAKE and RATTLE Algorithms for Rigid Water Models J. Comp. Chem. 13 (1992) pp. 952-962 -------- -------- --- Thank You --- -------- -------- Steepest Descents: Tolerance (Fmax) = 1.00000e+02 Number of steps = 100 Going to use C-settle (41607 waters) wo = 0.333333, wh =0.333333, wohh = 3, rc = 0.08165, ra = 0.0384897 rb = 0.0192449, rc2 = 0.1633, rone = 1, dHH = 0.1633, dOH = 0.1 Grid: 15 x 15 x 15 cells Configuring nonbonded kernels... Testing x86_64 SSE support... present. Step Time Lambda 0 0.00000 0.00000 ------------------------------------------------------- Program mdrun, VERSION 3.3.1 Source code file: nsgrid.c, line: 226 Range checking error: Explanation: During neighborsearching, we assign each particle to a grid based on its coordinates. If your system contains collisions or parameter errors that give particles very high velocities you might end up with some coordinates being +-Infinity or NaN (not-a-number). Obviously, we cannot put these on a grid, so this is usually where we detect those errors. Make sure your system is properly energy-minimized and that the potential energy seems reasonable before trying again. Variable ci has value -2147483648. It should have been within [ 0 .. 3375 ] Please report this to the mailing list ([email protected]) ------------------------------------------------------- At the end of this mail I have also pasted the em.mdp file I use to set up energy minimizations. I would really appreciate it if someone could help me address this Range checking error issue. Another type of error that I recently encountered occurs during position restrained dynamics simulations. The error is a constraint error in Lincs algorithm at a particular time step and usually is accompanied by a line that is similar to, (with time and atom number varying ) ----------------------------------------------------------------------------------------------------------------------------------------- t= 0.02ps Water molecule starting at atom 71500 can not be settled. Check for bad contacts and/or reduce the timestep.Wrote pdb files with previous and current coordinates ------------------------------------------------------------------------------------------------------------------------------------------- I have triend reducing the time step and I still get the same error. I have also pasted the pr.mdp file I use to set up and run position restrained dynamics. I would like some help in solving this lincs error issue. The original protease pdb file that I used for the above simulations has a small segment missing from chain A. This loop segment was highly disorderd in the cystal structure hence, coordinates for this 7 residue segment is missing in the pdb file. This missing segment is no where near where the ligand is bound on the protease. Does a missing segment cause problems during siumlations? Another general question on the genion function: Is there a way I could not have genion be interactive. My systems usually have a protein, a ligand and water, and I always choose group 13 (SOL) as the selection after running genion. I am asking this because there are times when I want to run the same protein with several different ligands and I would like a script to run through all gromacs steps and not have a particular step be interactive. Thanks for reading a long mail. Shyamala ------------------------------------------------------ em.mdp title = fws cpp = /usr/bin/cpp ; location of cpp define = -DFLEX_SPC constraints = none integrator = steep dt = 0.001 ; ps ! nsteps = 100 ; 100 steps of energy min nstlist = 10 ns_type = grid rlist = 1.0 coulombtype = PME rcoulomb = 1.0 vdwtype = cut-off rvdw = 1.4 table-extension = 3.0 fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 6 ewald_rtol = 1e-5 optimize_fft = yes ; ; Energy minimizing stuff ; emtol = 100.0 emstep = 0.01 ------------------------------------------------------- pr.mdp title = fws cpp = /usr/bin/cpp define = -DPOSRES constraints = all-bonds integrator = md dt = 0.002 ; ps ! nsteps = 5000 ; total 10.0 ps. nstcomm = 1 nstxout = 250 nstvout = 1000 nstfout = 0 nstlog = 10 nstenergy = 10 nstlist = 10 ns_type = grid rlist = 1.0 coulombtype = PME rcoulomb = 1.0 vdwtype = cut-off rvdw = 1.4 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 Tcoupl = berendsen tau_t = 0.1 0.1 tc_grps = protein non-protein ref_t = 300 300 ; Pressure coupling is on Pcoupl = berendsen pcoupltype = isotropic tau_p = 1.0 compressibility = 4.5e-5 ref_p = 1.0 ; Generate velocites is on at 300 K. gen_vel = yes gen_temp = 300.0 gen_seed = 173529 _______________________________________________ gmx-users mailing list [email protected] http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! 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