Re: [gmx-users] LINCS WARNING after good minimization and equilibration (NPT and NVT)
Thank you! I will try to change something and write to you about the result . -- Sincerely, Yulian Gavrilov -- gmx-users mailing listgmx-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
[gmx-users] LINCS WARNING after good minimization and equilibration (NPT and NVT)
Dear GROMACS users, I only begin to work with gromacs and now have some problems with tetra protein. I used AMBER force field and made several changes (in ffamber.rtp, specbond.dat, ffamber99bon.itp) to create an isopeptide bonds between monomers. Minimization and equilibration (NPT and NVT) were OK. But in MD (1.2 ns) I met a problem: __ Step 241687, time 483.374 (ps) LINCS WARNING relative constraint deviation after LINCS: rms nan, max inf (between atoms 2431 and 2432) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 2431 2432 90.00.1244 inf 0.1229 2428 2430 113.10.1010 64418817769472. 0.1010 2428 2429 105.70.1010 65196395593728. 0.1010 . t = 483.374 ps: Water molecule starting at atom 57549 can not be settled. Check for bad contacts and/or reduce the timestep. Wrote pdb files with previous and current coordinates Segmentation fault When I looked on step241686c.pdb in pymol, I found, that GLY that form one of isopeptide bonds exploded (it's atoms were far from the water box). I saw that a lot of people have a close problem, but usually they have it on the first steps. Also in my case minimization and equilibration were OK. I note some letters with the close problem, but I don't understand what to start with in my case. I kindly ask you to give me an idea or a link to a letter with the best solution. Simulation is based on tutorial: Lysozyme in Water. Justin Lemkul Thanks, Yulian HISTORY /gromacs-4.0.5/bin/pdb2gmx -f 3ALB_AMBER.pdb -o processed.gro -water tip3p -missing -merge /gromacs-4.0.5/bin/editconf -f processed.gro -o newbox.gro -c -d 1.0 -bt cubic /gromacs-4.0.5/bin/genbox -cp newbox.gro -cs spc216.gro -o solv.gro -p topol.top /gromacs-4.0.5/bin/grompp -f ions.mdp -c solv.gro -p topol.top -o ions.tpr /gromacs-4.0.5/bin/genion -s ions.tpr -o solv.gro -p topol.top -pname Na+ -np 24 /gromacs-4.0.5/bin/grompp -f minim.mdp -c solv.gro -p topol.top -o em.tpr /gromacs-4.0.5/bin/mdrun -v -deffnm em vmd em.gro /gromacs-4.0.5/bin/g_energy -f em.edr -o potential.xvg xmgrace potential.xvg /gromacs-4.0.5/bin/grompp -f nvt.mdp -c em.gro -p topol.top -o nvt.tpr /gromacs-4.0.5/bin/mdrun -v -deffnm nvt /gromacs-4.0.5/bin/g_energy -f nvt.edr xmgrace nvt.edr xmgrace energy.xvg /gromacs-4.0.5/bin/grompp -f npt.mdp -c nvt.gro -t nvt.cpt -p topol.top -o npt.tpr /gromacs-4.0.5/bin/mdrun -v -deffnm npt vmd npt.gro /gromacs-4.0.5/bin/g_energy -f npt.edr -o pressure.xvg xmgrace pressure.xvg /gromacs-4.0.5/bin/g_energy -f npt.edr -o density.xvg xmgrace density.xvg /gromacs-4.0.5/bin/grompp -f md.mdp -c npt.gro -t npt.cpt -p topol.top -o md_2ns.tpr /gromacs-4.0.5/bin/mdrun -v -deffnm md_2ns md.mdp title= AMBER Ub_tetra48 ; Run parameters integrator= md; leap-frog integrator nsteps= 60; 2 * 50 = 1000 ps, 1 ns dt= 0.002; 2 fs ; Output control nstxout= 1000; save coordinates every 2 ps nstvout= 1000; save velocities every 2 ps nstxtcout= 1000; xtc compressed trajectory output every 2 ps nstenergy= 1000; save energies every 2 ps nstlog= 1000; update log file every 2 ps ; Bond parameters continuation= yes; Restarting after NPT constraint_algorithm = lincs; holonomic constraints constraints= all-bonds; all bonds (even heavy atom-H bonds) constrained lincs_iter= 1; accuracy of LINCS lincs_order= 4; also related to accuracy ; Neighborsearching ns_type= grid; search neighboring grid cells nstlist= 5; 10 fs rlist= 1.0; short-range neighborlist cutoff (in nm) rcoulomb= 1.0; short-range electrostatic cutoff (in nm) rvdw= 1.0; short-range van der Waals cutoff (in nm) ; Electrostatics coulombtype= PME; Particle Mesh Ewald for long-range electrostatics pme_order= 4; cubic interpolation fourierspacing= 0.16; grid spacing for FFT ; Temperature coupling is on tcoupl= V-rescale; modified Berendsen thermostat tc-grps= Protein Non-Protein; two coupling groups - more accurate tau_t= 0.10.1; time constant, in ps ref_t= 300 300; reference temperature, one for each group, in K ; Pressure coupling is on pcoupl= Parrinello-Rahman; Pressure coupling on in NPT pcoupltype= isotropic; uniform scaling of box vectors tau_p= 2.0; time constant, in ps ref_p= 1.0; reference pressure, in bar compressibility = 4.5e-5; isothermal
Re: [gmx-users] LINCS WARNING after good minimization and equilibration (NPT and NVT)
zeppelin zeppelin wrote: Dear GROMACS users, I only begin to work with gromacs and now have some problems with tetra protein. I used AMBER force field and made several changes (in ffamber.rtp, specbond.dat, ffamber99bon.itp) to create an isopeptide bonds between monomers. Minimization and equilibration (NPT and NVT) were OK. But in MD (1.2 ns) I met a problem: __ Step 241687, time 483.374 (ps) LINCS WARNING relative constraint deviation after LINCS: rms nan, max inf (between atoms 2431 and 2432) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 2431 2432 90.00.1244 inf 0.1229 2428 2430 113.10.1010 64418817769472. 0.1010 2428 2429 105.70.1010 65196395593728. 0.1010 . t = 483.374 ps: Water molecule starting at atom 57549 can not be settled. Check for bad contacts and/or reduce the timestep. Wrote pdb files with previous and current coordinates Segmentation fault When I looked on step241686c.pdb in pymol, I found, that GLY that form one of isopeptide bonds exploded (it's atoms were far from the water box). I saw that a lot of people have a close problem, but usually they have it on the first steps. Also in my case minimization and equilibration were OK. I note some letters with the close problem, but I don't understand what to start with in my case. I kindly ask you to give me an idea or a link to a letter with the best solution. LINCS errors have many causes, and as such, there is no universal solution. The normal advice for solving this problem is as follows: http://www.gromacs.org/Documentation/Terminology/Blowing_Up#Diagnosing_an_Unstable_System I suspect with nstxout = 1000 you should have plenty of frames to watch at the point where the system becomes unstable. Looking at a single .pdb file from the crash will not show you how it happened; it just shows you what the result of the unstable system was. It sounds to me like whatever parameters you're using for your isopeptide bond are not stable, but you should decide that for yourself based on what you see in the trajectory. Simulation is based on tutorial: Lysozyme in Water. Justin Lemkul Note that the .mdp files I provide are for OPLS-AA, and may not be universally applicable. I make this caveat clear in the summary of the tutorial. You may have to change some of the parameters (particularly cutoffs, nstlist, time step, etc) to be compatible with AMBER. -Justin Thanks, Yulian HISTORY /gromacs-4.0.5/bin/pdb2gmx -f 3ALB_AMBER.pdb -o processed.gro -water tip3p -missing -merge /gromacs-4.0.5/bin/editconf -f processed.gro -o newbox.gro -c -d 1.0 -bt cubic /gromacs-4.0.5/bin/genbox -cp newbox.gro -cs spc216.gro -o solv.gro -p topol.top /gromacs-4.0.5/bin/grompp -f ions.mdp -c solv.gro -p topol.top -o ions.tpr /gromacs-4.0.5/bin/genion -s ions.tpr -o solv.gro -p topol.top -pname Na+ -np 24 /gromacs-4.0.5/bin/grompp -f minim.mdp -c solv.gro -p topol.top -o em.tpr /gromacs-4.0.5/bin/mdrun -v -deffnm em vmd em.gro /gromacs-4.0.5/bin/g_energy -f em.edr -o potential.xvg xmgrace potential.xvg /gromacs-4.0.5/bin/grompp -f nvt.mdp -c em.gro -p topol.top -o nvt.tpr /gromacs-4.0.5/bin/mdrun -v -deffnm nvt /gromacs-4.0.5/bin/g_energy -f nvt.edr xmgrace nvt.edr xmgrace energy.xvg /gromacs-4.0.5/bin/grompp -f npt.mdp -c nvt.gro -t nvt.cpt -p topol.top -o npt.tpr /gromacs-4.0.5/bin/mdrun -v -deffnm npt vmd npt.gro /gromacs-4.0.5/bin/g_energy -f npt.edr -o pressure.xvg xmgrace pressure.xvg /gromacs-4.0.5/bin/g_energy -f npt.edr -o density.xvg xmgrace density.xvg /gromacs-4.0.5/bin/grompp -f md.mdp -c npt.gro -t npt.cpt -p topol.top -o md_2ns.tpr /gromacs-4.0.5/bin/mdrun -v -deffnm md_2ns md.mdp title= AMBER Ub_tetra48 ; Run parameters integrator= md; leap-frog integrator nsteps= 60; 2 * 50 = 1000 ps, 1 ns dt= 0.002; 2 fs ; Output control nstxout= 1000; save coordinates every 2 ps nstvout= 1000; save velocities every 2 ps nstxtcout= 1000; xtc compressed trajectory output every 2 ps nstenergy= 1000; save energies every 2 ps nstlog= 1000; update log file every 2 ps ; Bond parameters continuation= yes; Restarting after NPT constraint_algorithm = lincs; holonomic constraints constraints= all-bonds; all bonds (even heavy atom-H bonds) constrained lincs_iter= 1; accuracy of LINCS lincs_order= 4; also related to accuracy ; Neighborsearching ns_type= grid; search neighboring grid cells nstlist= 5
