[gmx-users] regarding range checking error and constraint errors in Lincs algorithm
Matt Wyczalkowski
maw2 at cec.wustl.edu
Wed Dec 19 22:10:29 CET 2007
Funny enough, I came across the same problem just earlier today, with
the same large, negative ci value.
Setting the constraints as follows seemed to fix the problem,
constraints = all-bonds
Good luck,
Matt
shyamala iyer wrote:
> 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 (gmx-users at gromacs.org)
>
> -------------------------------------------------------
>
> 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 gmx-users at 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-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>
--
Matt Wyczalkowski
Doctoral Candidate, Biomedical Engineering
Pappu Lab: http://lima.wustl.edu
Washington University in St. Louis
maw2 at cec.wustl.edu
More information about the gromacs.org_gmx-users
mailing list