Re: [gmx-users] LINCS error
I get an error like this= Step 43230, time 86.46 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.033583, max 1.621884 (between atoms 2032 and 2030) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 2032 2030 90.00.4449 0.2622 0.1000 2031 2030 90.00.1949 0.1264 0.1000 Wrote pdb files with previous and current coordinates Step 43231, time 86.462 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.066301, max 3.173023 (between atoms 2032 and 2030) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 2032 2030 90.00.2622 0.4173 0.1000 2031 2030 89.90.1264 0.1675 0.1000 --- Program mdrun, VERSION 4.5.3 Source code file: constr.c, line: 176 Fatal error: Too many LINCS warnings (1001) If you know what you are doing you can adjust the lincs warning threshold in your mdp file or set the environment variable GMX_MAXCONSTRWARN to -1, but normally it is better to fix the problem For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- and my md.mdp file i altered goes like this= ; VARIOUS PREPROCESSING OPTIONS title= Production Simulation cpp = /lib/cpp ; RUN CONTROL PARAMETERS integrator = md tinit= 0 ; Starting time dt = 0.002 ; 2 femtosecond time step for integration nsteps = 250; Make it 10 ns ; OUTPUT CONTROL OPTIONS nstxout = 500 ; Writing full precision coordinates every nanosecond nstvout = 500 ; Writing velocities every nanosecond nstfout = 0 ; Not writing forces nstlog = 2500 ; Writing to the log file every step nstenergy= 2500 ; Writing out energy information every step nstxtcout= 500 ; Writing coordinates every 5 ps energygrps = Protein Non-Protein ; NEIGHBORSEARCHING PARAMETERS nstlist = 5 ns-type = Grid pbc = xyz rlist= 0.9 ; OPTIONS FOR ELECTROSTATICS AND VDW coulombtype = Reaction-Field rcoulomb = 1.4 epsilon_rf = 78 epsilon_r= 1 vdw-type = Cut-off rvdw = 1.4 ; Temperature coupling Tcoupl = Berendsen tc-grps = Protein Non-Protein tau_t= 0.1 0.1 ref_t= 300 300 ; Pressure coupling Pcoupl = Berendsen Pcoupltype = Isotropic tau_p= 1.0 compressibility = 4.5e-5 ref_p= 1.0 ; GENERATE VELOCITIES FOR STARTUP RUN gen_vel = no ; OPTIONS FOR BONDS constraints = all-bonds constraint-algorithm = Lincs unconstrained-start = yes lincs-order = 4 lincs-iter = 1 lincs-warnangle = 30 how should i rectify this. Please help On Sun, Dec 18, 2011 at 8:12 PM, Mark Abraham mark.abra...@anu.edu.auwrote: On 19/12/2011 1:05 AM, aiswarya pawar wrote: Hi users, I did energy minimization of a protein complex using the following minimization mdp file. See http://www.gromacs.org/Documentation/How-tos/Steps_to_Perform_a_Simulationfor general advice. ; Lines starting with ';' ARE COMMENTS ; Everything following ';' is also comment title = Energy Minimization ; Title of run ; The following line tell the program the standard locations where to find certain files cpp = /lib/cpp ; Preprocessor ; Define can be used to control processes define = -DFLEXIBLE ; Parameters describing what to do, when to stop and what to save integrator = steep ; Algorithm (steep = steepest descent minimization) emtol = 1000.0 ; Stop minimization when the maximum force 1.0 kJ/mol emstep = 0.01 nsteps = 5000 ; Maximum number of (minimization) steps to perform nstenergy = 10 ; Write energies to disk every nstenergy steps energygrps = Protein ; Which energy group(s) to write to disk ; Parameters describing how to find the neighbors of each atom and how to calculate the interactions nstlist = 10 ; Frequency to update the neighbor list and long range forces ns_type = grid ; Method to determine neighbor list (simple, grid) rlist = 1.0 ; Cut-off for making neighbor list (short range forces) coulombtype = PME ; Treatment of long range electrostatic interactions rcoulomb = 1.0 ; long range electrostatic cut-off rvdw = 1.4 ; long range Van der Waals cut-off constraints = none ; Bond types to replace by constraints pbc= xyz ; Periodic
Re: [gmx-users] LINCS error
aiswarya pawar wrote: I get an error like this= Step 43230, time 86.46 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.033583, max 1.621884 (between atoms 2032 and 2030) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 2032 2030 90.00.4449 0.2622 0.1000 2031 2030 90.00.1949 0.1264 0.1000 Wrote pdb files with previous and current coordinates Step 43231, time 86.462 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.066301, max 3.173023 (between atoms 2032 and 2030) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 2032 2030 90.00.2622 0.4173 0.1000 2031 2030 89.90.1264 0.1675 0.1000 --- Program mdrun, VERSION 4.5.3 Source code file: constr.c, line: 176 Fatal error: Too many LINCS warnings (1001) If you know what you are doing you can adjust the lincs warning threshold in your mdp file or set the environment variable GMX_MAXCONSTRWARN to -1, but normally it is better to fix the problem For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- and my md.mdp file i altered goes like this= ; VARIOUS PREPROCESSING OPTIONS title= Production Simulation cpp = /lib/cpp ; RUN CONTROL PARAMETERS integrator = md tinit= 0 ; Starting time dt = 0.002 ; 2 femtosecond time step for integration nsteps = 250; Make it 10 ns ; OUTPUT CONTROL OPTIONS nstxout = 500 ; Writing full precision coordinates every nanosecond nstvout = 500 ; Writing velocities every nanosecond nstfout = 0 ; Not writing forces nstlog = 2500 ; Writing to the log file every step nstenergy= 2500 ; Writing out energy information every step nstxtcout= 500 ; Writing coordinates every 5 ps energygrps = Protein Non-Protein ; NEIGHBORSEARCHING PARAMETERS nstlist = 5 ns-type = Grid pbc = xyz rlist= 0.9 ; OPTIONS FOR ELECTROSTATICS AND VDW coulombtype = Reaction-Field rcoulomb = 1.4 epsilon_rf = 78 epsilon_r= 1 vdw-type = Cut-off rvdw = 1.4 ; Temperature coupling Tcoupl = Berendsen tc-grps = Protein Non-Protein tau_t= 0.1 0.1 ref_t= 300 300 ; Pressure coupling Pcoupl = Berendsen Pcoupltype = Isotropic tau_p= 1.0 compressibility = 4.5e-5 ref_p= 1.0 ; GENERATE VELOCITIES FOR STARTUP RUN gen_vel = no ; OPTIONS FOR BONDS constraints = all-bonds constraint-algorithm = Lincs unconstrained-start = yes lincs-order = 4 lincs-iter = 1 lincs-warnangle = 30 how should i rectify this. Please help Please consult http://www.gromacs.org/Documentation/Errors#LINCS.2fSETTLE.2fSHAKE_warnings and/or the thousands of posts in the list archive that have been asked and answered on this topic. -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 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 error
Hi users, I did energy minimization of a protein complex using the following minimization mdp file. ; Lines starting with ';' ARE COMMENTS ; Everything following ';' is also comment title = Energy Minimization ; Title of run ; The following line tell the program the standard locations where to find certain files cpp = /lib/cpp ; Preprocessor ; Define can be used to control processes define = -DFLEXIBLE ; Parameters describing what to do, when to stop and what to save integrator = steep ; Algorithm (steep = steepest descent minimization) emtol = 1000.0 ; Stop minimization when the maximum force 1.0 kJ/mol emstep = 0.01 nsteps = 5000 ; Maximum number of (minimization) steps to perform nstenergy = 10 ; Write energies to disk every nstenergy steps energygrps = Protein ; Which energy group(s) to write to disk ; Parameters describing how to find the neighbors of each atom and how to calculate the interactions nstlist = 10 ; Frequency to update the neighbor list and long range forces ns_type = grid ; Method to determine neighbor list (simple, grid) rlist = 1.0 ; Cut-off for making neighbor list (short range forces) coulombtype = PME ; Treatment of long range electrostatic interactions rcoulomb = 1.0 ; long range electrostatic cut-off rvdw = 1.4 ; long range Van der Waals cut-off constraints = none ; Bond types to replace by constraints pbc= xyz ; Periodic Boundary Conditions (yes/no) and the pr.mdp = ; VARIOUS PREPROCESSING OPTIONS title= Position Restrained Molecular Dynamics define = -DPOSRES constraints = all-bonds integrator = md dt = 0.001 ; ps ! nsteps = 25000 ; total 50 ps. nstcomm = 10 nstxout = 500 ; collect data every 1 ps nstxtcout= 500 nstvout = 0 nstfout = 0 nstlist = 10 ns_type = grid rlist= 1.0 coulombtype = PME rcoulomb = 1.0 vdwtype = cut-off rvdw = 1.4 pme_order= 4 ewald_rtol = 1e-5 optimize_fft = yes DispCorr = no ; Berendsen temperature coupling is on Tcoupl = v-rescale tau_t= 0.1 0.1 tc-grps = protein non-protein ref_t= 300 300 ; Pressure coupling is on Pcoupl = parrinello-rahman 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 = -1 and md.mdp file = ; VARIOUS PREPROCESSING OPTIONS title= Position Restrained Molecular Dynamics ; RUN CONTROL PARAMETERS constraints = all-bonds integrator = md dt = 0.002 ; 2fs ! nsteps = 250 ; total 5000 ps. nstcomm = 10 nstxout = 500 ; collect data every 1 ps nstxtcout = 0 nstvout = 0 nstfout = 0 nstlist = 10 ns_type = grid rlist = 1.0 coulombtype = PME rcoulomb = 1.0 vdwtype = cut-off rvdw = 1.4 pme_order = 4 ewald_rtol = 1e-5 optimize_fft = yes DispCorr = no ; Berendsen temperature coupling is on Tcoupl = v-rescale tau_t = 0.1 0.1 tc-grps = protein non-protein ref_t = 300 300 ; Pressure coupling is on Pcoupl = parrinello-rahman 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 = -1 The minimization step went well. but while doing the final mdrun am getting LINCS error. i read through the numerous mailing list on grimaces but still couldn't understand how would i fix this. am getting this error for all the 10 protein complex i did minimization for. Please help. Thanks, Aiswarya -- 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
Re: [gmx-users] LINCS error
On 19/12/2011 1:05 AM, aiswarya pawar wrote: Hi users, I did energy minimization of a protein complex using the following minimization mdp file. See http://www.gromacs.org/Documentation/How-tos/Steps_to_Perform_a_Simulation for general advice. ; Lines starting with ';' ARE COMMENTS ; Everything following ';' is also comment title= Energy Minimization; Title of run ; The following line tell the program the standard locations where to find certain files cpp= /lib/cpp; Preprocessor ; Define can be used to control processes define = -DFLEXIBLE ; Parameters describing what to do, when to stop and what to save integrator= steep; Algorithm (steep = steepest descent minimization) emtol= 1000.0 ; Stop minimization when the maximum force 1.0 kJ/mol emstep = 0.01 nsteps= 5000; Maximum number of (minimization) steps to perform nstenergy= 10; Write energies to disk every nstenergy steps energygrps= Protein; Which energy group(s) to write to disk ; Parameters describing how to find the neighbors of each atom and how to calculate the interactions nstlist= 10; Frequency to update the neighbor list and long range forces ns_type= grid ; Method to determine neighbor list (simple, grid) rlist= 1.0; Cut-off for making neighbor list (short range forces) coulombtype= PME ; Treatment of long range electrostatic interactions rcoulomb= 1.0; long range electrostatic cut-off rvdw= 1.4; long range Van der Waals cut-off constraints= none; Bond types to replace by constraints pbc = xyz; Periodic Boundary Conditions (yes/no) and the pr.mdp = ; VARIOUS PREPROCESSING OPTIONS title= Position Restrained Molecular Dynamics define = -DPOSRES constraints = all-bonds integrator = md dt = 0.001 ; ps ! nsteps = 25000 ; total 50 ps. nstcomm = 10 nstxout = 500 ; collect data every 1 ps nstxtcout= 500 nstvout = 0 nstfout = 0 nstlist = 10 ns_type = grid rlist= 1.0 coulombtype = PME rcoulomb = 1.0 vdwtype = cut-off rvdw = 1.4 pme_order= 4 ewald_rtol = 1e-5 optimize_fft = yes DispCorr = no ; Berendsen temperature coupling is on Tcoupl = v-rescale tau_t= 0.1 0.1 tc-grps = protein non-protein ref_t= 300 300 ; Pressure coupling is on Pcoupl = parrinello-rahman 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 = -1 You are asking for trouble by generating velocities and doing position restraints with P-R pressure coupling in one step. It might work, but the workflow in the above link is safer. and md.mdp file = ; VARIOUS PREPROCESSING OPTIONS title= Position Restrained Molecular Dynamics ; RUN CONTROL PARAMETERS constraints = all-bonds integrator = md dt = 0.002 ; 2fs ! nsteps = 250 ; total 5000 ps. nstcomm = 10 nstxout = 500 ; collect data every 1 ps nstxtcout = 0 nstvout = 0 nstfout = 0 nstlist = 10 ns_type = grid rlist = 1.0 coulombtype = PME rcoulomb = 1.0 vdwtype = cut-off rvdw = 1.4 pme_order = 4 ewald_rtol = 1e-5 optimize_fft = yes DispCorr = no ; Berendsen temperature coupling is on Tcoupl = v-rescale tau_t = 0.1 0.1 tc-grps = protein non-protein ref_t = 300 300 ; Pressure coupling is on Pcoupl = parrinello-rahman 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 = -1 Why are you re-generating non-equilibrium velocities after equilibrating them? Mark The minimization step went well. but while doing the final mdrun am getting LINCS error. i read through the numerous mailing list on grimaces but still couldn't understand how would i fix this. am getting this error for all the 10 protein complex i did minimization for. Please help. Thanks, Aiswarya -- 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
Re: [gmx-users] LINCS error- 4.5.4 installation?
On 4/30/2011 9:06 AM, Juliette N. wrote: Dear experts, I just tried the command mpirun -np 4 mdrun on 4.5.4 but after a few steps I get LINCS error: step 400, will finish Sat Apr 30 05:20:45 2011 Step 750, time 1.5 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 10.116560, max 72.359520 (between atoms 314 and 315) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 301302 61.00.1090 0.1841 0.1090 I tried to run using the same input files on 4.0.7 and simulation worked fine. I mean the LINCS is not because of flawed topology or instability issue. I am wondering this is happening because of MPI or installation ..Please help! Normally, a successful MPI installation would have produced an mdrun_mpi executable, not mdrun. 15 minutes before this email you didn't manage to configure successfully with --enable-mpi. So probably you are not running in parallel. Look at the number of .log files produced, and their first line. Regarding the LINCS error, your simulation was probably marginally stable, and got lucky with the integration in 4.0.7 and unlucky in 4.5. That's life - you should consider the management strategies here http://www.gromacs.org/Documentation/Terminology/Blowing_Up Mark -- 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
Re: [gmx-users] LINCS error
Yongchul Chung wrote:
Hi again gmx-users,
I ran into LINCS error again when I tried to incorporate pressure
scaling parameters.
It seems like the initial pressure and temperature is erroneously large
as shown in the md.log file below. can anyone tell me how to fix this?
Did you run energy minimization first?
-Justin
Thanks
Input Parameters:
integrator = md
nsteps = 10
init_step= 0
ns_type = Grid
nstlist = 10
ndelta = 2
nstcomm = 1
comm_mode= Linear
nstlog = 10
nstxout = 500
nstvout = 1000
nstfout = 0
nstenergy= 10
nstxtcout= 0
init_t = 0
delta_t = 0.002
xtcprec = 1000
nkx = 0
nky = 0
nkz = 0
pme_order= 4
ewald_rtol = 1e-05
ewald_geometry = 0
epsilon_surface = 0
optimize_fft = TRUE
ePBC = xyz
bPeriodicMols= FALSE
bContinuation= FALSE
bShakeSOR= FALSE
etc = V-rescale
epc = Berendsen
epctype = Isotropic
tau_p= 1
ref_p (3x3):
ref_p[0]={ 1.01325e+00, 0.0e+00, 0.0e+00}
ref_p[1]={ 0.0e+00, 1.01325e+00, 0.0e+00}
ref_p[2]={ 0.0e+00, 0.0e+00, 1.01325e+00}
compress (3x3):
compress[0]={ 4.5e-03, 0.0e+00, 0.0e+00}
compress[1]={ 0.0e+00, 4.5e-03, 0.0e+00}
compress[2]={ 0.0e+00, 0.0e+00, 4.5e-03}
refcoord_scaling = No
posres_com (3):
posres_com[0]= 0.0e+00
posres_com[1]= 0.0e+00
posres_com[2]= 0.0e+00
posres_comB (3):
posres_comB[0]= 0.0e+00
posres_comB[1]= 0.0e+00
posres_comB[2]= 0.0e+00
andersen_seed= 815131
rlist= 1
rtpi = 0.05
coulombtype = Cut-off
rcoulomb_switch = 0
rcoulomb = 1.4
vdwtype = Cut-off
rvdw_switch = 0
rvdw = 1.4
epsilon_r= 1
epsilon_rf = 1
tabext = 1
implicit_solvent = No
gb_algorithm = Still
gb_epsilon_solvent = 80
nstgbradii = 1
rgbradii = 2
gb_saltconc = 0
gb_obc_alpha = 1
gb_obc_beta = 0.8
gb_obc_gamma = 4.85
sa_surface_tension = 2.092
DispCorr = No
free_energy = no
init_lambda = 0
sc_alpha = 0
sc_power = 0
sc_sigma = 0.3
delta_lambda = 0
nwall= 0
wall_type= 9-3
wall_atomtype[0] = -1
wall_atomtype[1] = -1
wall_density[0] = 0
wall_density[1] = 0
wall_ewald_zfac = 3
pull = no
disre= No
disre_weighting = Conservative
disre_mixed = FALSE
dr_fc= 1000
dr_tau = 0
nstdisreout = 100
orires_fc= 0
orires_tau = 0
nstorireout = 100
dihre-fc = 1000
em_stepsize = 0.01
em_tol = 10
niter= 20
fc_stepsize = 0
nstcgsteep = 1000
nbfgscorr= 10
ConstAlg = Lincs
shake_tol= 0.0001
lincs_order = 4
lincs_warnangle = 30
lincs_iter = 1
bd_fric = 0
ld_seed = 1993
cos_accel= 0
deform (3x3):
deform[0]={ 0.0e+00, 0.0e+00, 0.0e+00}
deform[1]={ 0.0e+00, 0.0e+00, 0.0e+00}
deform[2]={ 0.0e+00, 0.0e+00, 0.0e+00}
userint1 = 0
userint2 = 0
userint3 = 0
userint4 = 0
userreal1= 0
userreal2= 0
userreal3= 0
userreal4= 0
grpopts:
nrdf: 11297
ref_t: 300
tau_t: 0.1
anneal: No
ann_npoints: 0
acc: 0 0 0
nfreeze: N N N
energygrp_flags[ 0]: 0
efield-x:
n = 0
efield-xt:
n = 0
efield-y:
n = 0
efield-yt:
n = 0
efield-z:
n = 0
efield-zt:
n = 0
bQMMM= FALSE
QMconstraints= 0
QMMMscheme = 0
scalefactor = 1
qm_opts:
ngQM = 0
Table routines are used for coulomb: FALSE
Table routines are used for vdw: FALSE
Cut-off's: NS: 1 Coulomb: 1.4 LJ: 1.4
System total charge: -0.000
Configuring
Re: [gmx-users] LINCS error
Yongchul Chung wrote: yes I carried out energy minimization and used following parameters. OK, so what values of potential energy and maximum force did EM achieve? -Justin title = FWS cpp = /usr/bin/cpp ; the c pre-processor define = -DFLEXIBLE constraints = none integrator = steep dt = 0.002; ps ! nsteps = 1000 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 = 4 ewald_rtol = 1e-5 optimize_fft = yes ; ; Energy minimizing stuff ; emtol = 500 emstep = 0.01 -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar 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 listgmx-users@gromacs.org http://lists.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
Re: [gmx-users] LINCS error
After EM, I got: Potential Energy = 1.7242092e+05 Maximum force = 2.1079963e+03 on atom 675 Norm of force = 5.9417034e+01 I think my system size is too big compared to the box size so I am going to run the simulation with smaller number of molecules to see whether this helps or not. On Fri, Oct 9, 2009 at 11:22 AM, Justin A. Lemkul jalem...@vt.edu wrote: Yongchul Chung wrote: yes I carried out energy minimization and used following parameters. OK, so what values of potential energy and maximum force did EM achieve? -Justin title = FWS cpp = /usr/bin/cpp ; the c pre-processor define = -DFLEXIBLE constraints = none integrator = steep dt = 0.002; ps ! nsteps = 1000 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 = 4 ewald_rtol = 1e-5 optimize_fft = yes ; ; Energy minimizing stuff ; emtol = 500 emstep = 0.01 -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar 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 listgmx-users@gromacs.org http://lists.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 -- Yongchul Greg Chung Graduate Student Dept. of Chemical Engineering, Case Western Reserve University ___ gmx-users mailing listgmx-users@gromacs.org http://lists.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
Re: [gmx-users] LINCS error
Yongchul Chung wrote: After EM, I got: Potential Energy = 1.7242092e+05 Maximum force = 2.1079963e+03 on atom 675 Norm of force = 5.9417034e+01 I think my system size is too big compared to the box size so I am going to run the simulation with smaller number of molecules to see whether this helps or not. Well, it could be that things are too jam-packed. Note that you have an extremely repulsive potential energy, and a very large Fmax. Using the atom number printed, you should be able to deduce the location of this large force, and hopefully the source, which is likely causing your explosion. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar 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 listgmx-users@gromacs.org http://lists.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
[gmx-users] LINCS error
Hi all,
I am trying to simulate 100 molecules of n-alkane molecules but keep
receiving LINC errors.
When I completed steepest descent I received following msg:
Steepest Descents converged to Fmax 500 in 819 steps
Potential Energy = 1.7174361e+05
Maximum force = 4.4903098e+02 on atom 172
Norm of force = 3.0003010e+01
Then I performed mdrun with the output of this file and gets LINCS warning:
Input Parameters:
integrator = md
nsteps = 8000
init_step= 0
ns_type = Grid
nstlist = 10
ndelta = 2
nstcomm = 1
comm_mode= Linear
nstlog = 10
nstxout = 250
nstvout = 1000
nstfout = 0
nstenergy= 10
nstxtcout= 0
init_t = 0
delta_t = 0.01
xtcprec = 1000
nkx = 125
nky = 125
nkz = 125
pme_order= 4
ewald_rtol = 1e-05
ewald_geometry = 0
epsilon_surface = 0
optimize_fft = TRUE
ePBC = xyz
bPeriodicMols= FALSE
bContinuation= FALSE
bShakeSOR= FALSE
etc = V-rescale
epc = No
epctype = Isotropic
tau_p= 1
ref_p (3x3):
ref_p[0]={ 0.0e+00, 0.0e+00, 0.0e+00}
ref_p[1]={ 0.0e+00, 0.0e+00, 0.0e+00}
ref_p[2]={ 0.0e+00, 0.0e+00, 0.0e+00}
compress (3x3):
compress[0]={ 0.0e+00, 0.0e+00, 0.0e+00}
compress[1]={ 0.0e+00, 0.0e+00, 0.0e+00}
compress[2]={ 0.0e+00, 0.0e+00, 0.0e+00}
refcoord_scaling = No
posres_com (3):
posres_com[0]= 0.0e+00
posres_com[1]= 0.0e+00
posres_com[2]= 0.0e+00
posres_comB (3):
posres_comB[0]= 0.0e+00
posres_comB[1]= 0.0e+00
posres_comB[2]= 0.0e+00
andersen_seed= 815131
rlist= 1
rtpi = 0.05
coulombtype = PME
rcoulomb_switch = 0
rcoulomb = 1
vdwtype = Cut-off
rvdw_switch = 0
rvdw = 2
epsilon_r= 1
epsilon_rf = 1
tabext = 1
implicit_solvent = No
gb_algorithm = Still
gb_epsilon_solvent = 80
nstgbradii = 1
rgbradii = 2
gb_saltconc = 0
gb_obc_alpha = 1
gb_obc_beta = 0.8
gb_obc_gamma = 4.85
sa_surface_tension = 2.092
DispCorr = No
free_energy = no
init_lambda = 0
sc_alpha = 0
sc_power = 0
sc_sigma = 0.3
delta_lambda = 0
nwall= 0
wall_type= 9-3
wall_atomtype[0] = -1
wall_atomtype[1] = -1
wall_density[0] = 0
wall_density[1] = 0
wall_ewald_zfac = 3
pull = no
disre= No
disre_weighting = Conservative
disre_mixed = FALSE
dr_fc= 1000
dr_tau = 0
nstdisreout = 100
orires_fc= 0
orires_tau = 0
nstorireout = 100
dihre-fc = 1000
em_stepsize = 0.01
em_tol = 10
niter= 20
fc_stepsize = 0
nstcgsteep = 1000
nbfgscorr= 10
ConstAlg = Lincs
shake_tol= 0.0001
lincs_order = 4
lincs_warnangle = 30
lincs_iter = 1
bd_fric = 0
ld_seed = 1993
cos_accel= 0
deform (3x3):
deform[0]={ 0.0e+00, 0.0e+00, 0.0e+00}
deform[1]={ 0.0e+00, 0.0e+00, 0.0e+00}
deform[2]={ 0.0e+00, 0.0e+00, 0.0e+00}
userint1 = 0
userint2 = 0
userint3 = 0
userint4 = 0
userreal1= 0
userreal2= 0
userreal3= 0
userreal4= 0
grpopts:
nrdf: 11297
ref_t: 300
tau_t: 0.1
anneal: No
ann_npoints: 0
acc: 0 0 0
nfreeze: N N N
energygrp_flags[ 0]: 0
efield-x:
n = 0
efield-xt:
n = 0
efield-y:
n = 0
efield-yt:
n = 0
efield-z:
n = 0
efield-zt:
n = 0
bQMMM= FALSE
QMconstraints= 0
QMMMscheme = 0
scalefactor = 1
qm_opts:
ngQM = 0
Table routines are used for coulomb: TRUE
Table routines are used for vdw: FALSE
Will do PME sum in reciprocal
Re: [gmx-users] LINCS error
delta_t = 0.01
You are using a 10 fs timestep!!! That is way too long. Standard is 2
(with bond constraints).
Yongchul Chung wrote:
Hi all,
I am trying to simulate 100 molecules of n-alkane molecules but keep
receiving LINC errors.
When I completed steepest descent I received following msg:
Steepest Descents converged to Fmax 500 in 819 steps
Potential Energy = 1.7174361e+05
Maximum force = 4.4903098e+02 on atom 172
Norm of force = 3.0003010e+01
Then I performed mdrun with the output of this file and gets LINCS
warning:
Input Parameters:
integrator = md
nsteps = 8000
init_step= 0
ns_type = Grid
nstlist = 10
ndelta = 2
nstcomm = 1
comm_mode= Linear
nstlog = 10
nstxout = 250
nstvout = 1000
nstfout = 0
nstenergy= 10
nstxtcout= 0
init_t = 0
delta_t = 0.01
xtcprec = 1000
nkx = 125
nky = 125
nkz = 125
pme_order= 4
ewald_rtol = 1e-05
ewald_geometry = 0
epsilon_surface = 0
optimize_fft = TRUE
ePBC = xyz
bPeriodicMols= FALSE
bContinuation= FALSE
bShakeSOR= FALSE
etc = V-rescale
epc = No
epctype = Isotropic
tau_p= 1
ref_p (3x3):
ref_p[0]={ 0.0e+00, 0.0e+00, 0.0e+00}
ref_p[1]={ 0.0e+00, 0.0e+00, 0.0e+00}
ref_p[2]={ 0.0e+00, 0.0e+00, 0.0e+00}
compress (3x3):
compress[0]={ 0.0e+00, 0.0e+00, 0.0e+00}
compress[1]={ 0.0e+00, 0.0e+00, 0.0e+00}
compress[2]={ 0.0e+00, 0.0e+00, 0.0e+00}
refcoord_scaling = No
posres_com (3):
posres_com[0]= 0.0e+00
posres_com[1]= 0.0e+00
posres_com[2]= 0.0e+00
posres_comB (3):
posres_comB[0]= 0.0e+00
posres_comB[1]= 0.0e+00
posres_comB[2]= 0.0e+00
andersen_seed= 815131
rlist= 1
rtpi = 0.05
coulombtype = PME
rcoulomb_switch = 0
rcoulomb = 1
vdwtype = Cut-off
rvdw_switch = 0
rvdw = 2
epsilon_r= 1
epsilon_rf = 1
tabext = 1
implicit_solvent = No
gb_algorithm = Still
gb_epsilon_solvent = 80
nstgbradii = 1
rgbradii = 2
gb_saltconc = 0
gb_obc_alpha = 1
gb_obc_beta = 0.8
gb_obc_gamma = 4.85
sa_surface_tension = 2.092
DispCorr = No
free_energy = no
init_lambda = 0
sc_alpha = 0
sc_power = 0
sc_sigma = 0.3
delta_lambda = 0
nwall= 0
wall_type= 9-3
wall_atomtype[0] = -1
wall_atomtype[1] = -1
wall_density[0] = 0
wall_density[1] = 0
wall_ewald_zfac = 3
pull = no
disre= No
disre_weighting = Conservative
disre_mixed = FALSE
dr_fc= 1000
dr_tau = 0
nstdisreout = 100
orires_fc= 0
orires_tau = 0
nstorireout = 100
dihre-fc = 1000
em_stepsize = 0.01
em_tol = 10
niter= 20
fc_stepsize = 0
nstcgsteep = 1000
nbfgscorr= 10
ConstAlg = Lincs
shake_tol= 0.0001
lincs_order = 4
lincs_warnangle = 30
lincs_iter = 1
bd_fric = 0
ld_seed = 1993
cos_accel= 0
deform (3x3):
deform[0]={ 0.0e+00, 0.0e+00, 0.0e+00}
deform[1]={ 0.0e+00, 0.0e+00, 0.0e+00}
deform[2]={ 0.0e+00, 0.0e+00, 0.0e+00}
userint1 = 0
userint2 = 0
userint3 = 0
userint4 = 0
userreal1= 0
userreal2= 0
userreal3= 0
userreal4= 0
grpopts:
nrdf: 11297
ref_t: 300
tau_t: 0.1
anneal: No
ann_npoints: 0
acc: 0 0 0
nfreeze: N N N
energygrp_flags[ 0]: 0
efield-x:
n = 0
efield-xt:
n = 0
efield-y:
n = 0
efield-yt:
n = 0
efield-z:
n = 0
efield-zt:
n = 0
bQMMM= FALSE
QMconstraints= 0
QMMMscheme = 0
scalefactor
Re: [gmx-users] LINCS error
Hi guys,
As Justin pointed out, it was the problem with md simulation blowing up. I
also had coloumbtype=PME and had to switch to cut-off to make my simulation
run faster.
Thanks for all the help.
On Thu, Oct 8, 2009 at 11:44 AM, Jochen Hub joc...@xray.bmc.uu.se wrote:
delta_t = 0.01
You are using a 10 fs timestep!!! That is way too long. Standard is 2 (with
bond constraints).
Yongchul Chung wrote:
Hi all,
I am trying to simulate 100 molecules of n-alkane molecules but keep
receiving LINC errors.
When I completed steepest descent I received following msg:
Steepest Descents converged to Fmax 500 in 819 steps
Potential Energy = 1.7174361e+05
Maximum force = 4.4903098e+02 on atom 172
Norm of force = 3.0003010e+01
Then I performed mdrun with the output of this file and gets LINCS
warning:
Input Parameters:
integrator = md
nsteps = 8000
init_step= 0
ns_type = Grid
nstlist = 10
ndelta = 2
nstcomm = 1
comm_mode= Linear
nstlog = 10
nstxout = 250
nstvout = 1000
nstfout = 0
nstenergy= 10
nstxtcout= 0
init_t = 0
delta_t = 0.01
xtcprec = 1000
nkx = 125
nky = 125
nkz = 125
pme_order= 4
ewald_rtol = 1e-05
ewald_geometry = 0
epsilon_surface = 0
optimize_fft = TRUE
ePBC = xyz
bPeriodicMols= FALSE
bContinuation= FALSE
bShakeSOR= FALSE
etc = V-rescale
epc = No
epctype = Isotropic
tau_p= 1
ref_p (3x3):
ref_p[0]={ 0.0e+00, 0.0e+00, 0.0e+00}
ref_p[1]={ 0.0e+00, 0.0e+00, 0.0e+00}
ref_p[2]={ 0.0e+00, 0.0e+00, 0.0e+00}
compress (3x3):
compress[0]={ 0.0e+00, 0.0e+00, 0.0e+00}
compress[1]={ 0.0e+00, 0.0e+00, 0.0e+00}
compress[2]={ 0.0e+00, 0.0e+00, 0.0e+00}
refcoord_scaling = No
posres_com (3):
posres_com[0]= 0.0e+00
posres_com[1]= 0.0e+00
posres_com[2]= 0.0e+00
posres_comB (3):
posres_comB[0]= 0.0e+00
posres_comB[1]= 0.0e+00
posres_comB[2]= 0.0e+00
andersen_seed= 815131
rlist= 1
rtpi = 0.05
coulombtype = PME
rcoulomb_switch = 0
rcoulomb = 1
vdwtype = Cut-off
rvdw_switch = 0
rvdw = 2
epsilon_r= 1
epsilon_rf = 1
tabext = 1
implicit_solvent = No
gb_algorithm = Still
gb_epsilon_solvent = 80
nstgbradii = 1
rgbradii = 2
gb_saltconc = 0
gb_obc_alpha = 1
gb_obc_beta = 0.8
gb_obc_gamma = 4.85
sa_surface_tension = 2.092
DispCorr = No
free_energy = no
init_lambda = 0
sc_alpha = 0
sc_power = 0
sc_sigma = 0.3
delta_lambda = 0
nwall= 0
wall_type= 9-3
wall_atomtype[0] = -1
wall_atomtype[1] = -1
wall_density[0] = 0
wall_density[1] = 0
wall_ewald_zfac = 3
pull = no
disre= No
disre_weighting = Conservative
disre_mixed = FALSE
dr_fc= 1000
dr_tau = 0
nstdisreout = 100
orires_fc= 0
orires_tau = 0
nstorireout = 100
dihre-fc = 1000
em_stepsize = 0.01
em_tol = 10
niter= 20
fc_stepsize = 0
nstcgsteep = 1000
nbfgscorr= 10
ConstAlg = Lincs
shake_tol= 0.0001
lincs_order = 4
lincs_warnangle = 30
lincs_iter = 1
bd_fric = 0
ld_seed = 1993
cos_accel= 0
deform (3x3):
deform[0]={ 0.0e+00, 0.0e+00, 0.0e+00}
deform[1]={ 0.0e+00, 0.0e+00, 0.0e+00}
deform[2]={ 0.0e+00, 0.0e+00, 0.0e+00}
userint1 = 0
userint2 = 0
userint3 = 0
userint4 = 0
userreal1= 0
userreal2= 0
userreal3= 0
userreal4= 0
grpopts:
nrdf: 11297
ref_t: 300
tau_t: 0.1
anneal: No
ann_npoints: 0
acc: 0 0 0
nfreeze: N N N
Re: [gmx-users] LINCS error
Yongchul Chung wrote:
Hi guys,
As Justin pointed out, it was the problem with md simulation blowing up.
I also had coloumbtype=PME and had to switch to cut-off to make my
simulation run faster.
And it will be substantially less accurate than using PME. I would say Jochen's
advice is the best - reduce the time step to something reasonable, and use PME.
-Justin
Thanks for all the help.
On Thu, Oct 8, 2009 at 11:44 AM, Jochen Hub joc...@xray.bmc.uu.se
mailto:joc...@xray.bmc.uu.se wrote:
delta_t = 0.01
You are using a 10 fs timestep!!! That is way too long. Standard is
2 (with bond constraints).
Yongchul Chung wrote:
Hi all,
I am trying to simulate 100 molecules of n-alkane molecules but
keep receiving LINC errors.
When I completed steepest descent I received following msg:
Steepest Descents converged to Fmax 500 in 819 steps
Potential Energy = 1.7174361e+05
Maximum force = 4.4903098e+02 on atom 172
Norm of force = 3.0003010e+01
Then I performed mdrun with the output of this file and gets
LINCS warning:
Input Parameters:
integrator = md
nsteps = 8000
init_step= 0
ns_type = Grid
nstlist = 10
ndelta = 2
nstcomm = 1
comm_mode= Linear
nstlog = 10
nstxout = 250
nstvout = 1000
nstfout = 0
nstenergy= 10
nstxtcout= 0
init_t = 0
delta_t = 0.01
xtcprec = 1000
nkx = 125
nky = 125
nkz = 125
pme_order= 4
ewald_rtol = 1e-05
ewald_geometry = 0
epsilon_surface = 0
optimize_fft = TRUE
ePBC = xyz
bPeriodicMols= FALSE
bContinuation= FALSE
bShakeSOR= FALSE
etc = V-rescale
epc = No
epctype = Isotropic
tau_p= 1
ref_p (3x3):
ref_p[0]={ 0.0e+00, 0.0e+00, 0.0e+00}
ref_p[1]={ 0.0e+00, 0.0e+00, 0.0e+00}
ref_p[2]={ 0.0e+00, 0.0e+00, 0.0e+00}
compress (3x3):
compress[0]={ 0.0e+00, 0.0e+00, 0.0e+00}
compress[1]={ 0.0e+00, 0.0e+00, 0.0e+00}
compress[2]={ 0.0e+00, 0.0e+00, 0.0e+00}
refcoord_scaling = No
posres_com (3):
posres_com[0]= 0.0e+00
posres_com[1]= 0.0e+00
posres_com[2]= 0.0e+00
posres_comB (3):
posres_comB[0]= 0.0e+00
posres_comB[1]= 0.0e+00
posres_comB[2]= 0.0e+00
andersen_seed= 815131
rlist= 1
rtpi = 0.05
coulombtype = PME
rcoulomb_switch = 0
rcoulomb = 1
vdwtype = Cut-off
rvdw_switch = 0
rvdw = 2
epsilon_r= 1
epsilon_rf = 1
tabext = 1
implicit_solvent = No
gb_algorithm = Still
gb_epsilon_solvent = 80
nstgbradii = 1
rgbradii = 2
gb_saltconc = 0
gb_obc_alpha = 1
gb_obc_beta = 0.8
gb_obc_gamma = 4.85
sa_surface_tension = 2.092
DispCorr = No
free_energy = no
init_lambda = 0
sc_alpha = 0
sc_power = 0
sc_sigma = 0.3
delta_lambda = 0
nwall= 0
wall_type= 9-3
wall_atomtype[0] = -1
wall_atomtype[1] = -1
wall_density[0] = 0
wall_density[1] = 0
wall_ewald_zfac = 3
pull = no
disre= No
disre_weighting = Conservative
disre_mixed = FALSE
dr_fc= 1000
dr_tau = 0
nstdisreout = 100
orires_fc= 0
orires_tau = 0
nstorireout = 100
dihre-fc = 1000
em_stepsize = 0.01
em_tol
[gmx-users] LINCS error
Hi, I am trying to simulate a peptide whose structure is yet to be validated experimentally. It has 3 protonated lysine residues. I have used oplsaa force filed with spc water model and had added 3 CL ions into the box. Everything works fine till energy minimisation but after that during position restricted dynamics, I encounter segmentation fault that states relative constraint deviation after LINCS: I again energy minimized the structure and then during the position restrained dynamics run I get the error Can't settle water molecule starting with .. While going through the Suggestions for creating helix in octane simulation system in gromacs I got the suggestion to remove that particular water molecule from the starting configuration and energy minimising it again. I removed the molecule from the already energy minimised structure, updated the topology file and again ran the position restrained dynamics. But again the same error comes that a particular water molecule can't be settled. I had tried to use different energy minimisation processes but still I am unable to fix this problem If I get any help , it will be highly beneficial. Sarbani ___ gmx-users mailing listgmx-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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] LINCS error
sarbani chattopadhyay wrote: Hi, I am trying to simulate a peptide whose structure is yet to be validated experimentally. It has 3 protonated lysine residues. I have used oplsaa force filed with spc water model and had added 3 CL ions into the box. Everything works fine till energy minimisation but after that during position restricted dynamics, I encounter segmentation fault that states relative constraint deviation after LINCS: I again energy minimized the structure and then during the position restrained dynamics run I get the error Can't settle water molecule starting with .. While going through the Suggestions for creating helix in octane simulation system in gromacs I got the suggestion to remove that particular water molecule from the starting configuration and energy minimising it again. I removed the molecule from the already energy minimised structure, updated the topology file and again ran the position restrained dynamics. But again the same error comes that a particular water molecule can't be settled. I had tried to use different energy minimisation processes but still I am unable to fix this problem Have you tried searching the archives for other solutions? Searching for cannot settle water molecule and LINCS warning together return almost 600 results. This is probably one of the most common problems reported to this list. Deleting the problematic water molecule is almost never the solution. For some more reference, see here: http://wiki.gromacs.org/index.php/Errors#LINCS.2FSETTLE.2FSHAKE_warnings Visualize the trajectory, see where things are blowing up, and re-evaluate what you are doing. -Justin If I get any help , it will be highly beneficial. Sarbani Ebay http://adworks.rediff.com/cgi-bin/AdWorks/click.cgi/www.rediff.com/signature-default.htm/[EMAIL PROTECTED]/2401775_2394076/2397136/1?PARTNER=3OAS_QUERY=null ___ gmx-users mailing listgmx-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 [EMAIL PROTECTED] 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 listgmx-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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Lincs error and explosion of the system
Dear users, I have a problem on runningMD of 146 LC molecules system. I do not do the energy minimisation. I use NVT ensemble to equilibrate my system.My topology was created using PRODRG beta server. After the creation of my systems box (on top of each other) 1. editconf -f lc -bt d -box 1.3 0.02 0.02 -princ -c -d 0.5 -rvdw 0.12 -o lcc 2. genconf -f lcc -nbox 8 8 8 -dist 0 0 0 -nmolat 27 -o lc512 I put inside another(a little bigger) molecule 3. editconf -f sl -bt c -box 6 -princ -c -d 2.5 -rvdw 0.12 -o sll 4. genbox -cp sll -cs lc512 -o slw -p sl then create tpr 5. grompp -v -np 32 -shuffle -sort -f eq.mdp -c slw -p sl -o topol.tpr and submit the job I always get my system exploding Initializing LINear Constraint Solver number of constraints is 122 average number of constraints coupled to one constraint is 3.0 Rel. Constraint Deviation: Max between atoms RMS Before LINCS 0.086035 40 39 0.026421 After LINCS 0.000704 103 104 0.000292 Energies (kJ/mol) G96Angle Proper Dih. Improper Dih. LJ-14 Coulomb-14 2.76783e+03 8.11377e+01 8.21662e+01 3.98602e+04 5.57164e+03 LJ (SR) LJ (LR) Coulomb (SR) Coul. recip. Potential 2.71048e+03 -1.88575e+02 -3.38992e+03 -3.62073e+04 1.12877e+04 Kinetic En. Total Energy Temperature Pressure (bar) 6.65517e+04 7.78394e+04 2.06669e+03 1.75872e+05 Step 86, time 0.172 (ps) LINCS WARNING relative constraint deviation after LINCS: max 96.909290 (between atoms 85 and 86) rms 10.933811 bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 77 78 113.7 0.1390 0.5917 0.1390 77 87 116.3 0.1390 0.5570 0.1390 78 79 109.8 0.1090 0.5917 0.1090 78 80 104.4 0.1390 1.2899 0.1390 80 81 93.6 0.1090 5.0458 0.1090 82 80 99.8 0.1390 3.9224 0.1390 82 83 100.5 0.1430 3.8921 0.1430 82 85 99.9 0.1390 3.9638 0.1390 83 84 103.4 0.1140 3.1119 0.1140 85 86 91.7 0.1090 10.6721 0.1090 85 87 100.2 0.1390 1.7797 0.1390 87 88 110.3 0.1090 0.5717 0.1090 Constraint error in algorithm Lincs at step 86 Wrote pdb files with previous and current coordinates Large VCM(group rest): -949890684120872786061526585043023133196136319944012857455888493019588547485855908650717825011817737590092000256377384500897124503083675335640562545921274578670325230339034153228858928503740516247758241500986457604229169152.0, -770017767340537250834106819849535443794415171890886583459517725651760798703652487434834859771194101005699859793685064099787214560958505758284878533509661264882479706501126070295847653568962516830194295490734095350104064.0, -17482030675841594076114066100363479435124387445824631353703195421406478322250794440904806833364056039859394683424411714469447896344546474426178109668279235955517800609185251692588873229116161214420413237478774727134943379456.0, ekin-cm: inf MDP file title = molecular dynamics cpp = /usr/bin/cpp include = -I../top ; RUN CONTROL PARAMETERS integrator = md dt = 0.002 ;ps nsteps = 500 ;10 ns ;comm_mode = Angular ;remove center of mass translation and rotation around the center of mass nstcomm = 1 ;number of steps for center of mass motion removal ; OUTPUT CONTROL OPTIONS nstxout = 100 ;every0.2 ps nstvout = 100 nstfout = 0 nstlog = 100 ;Output frequency to write energies to log file nstenergy = 100 ;Output frequency to write energies to energy file energygrps = MMM DRG ;Selection of energy groups ; NEIGHBOR SEARCHING PARAMETERS nstlist = 1 ;update frequency ns_type = grid ;algorithm (simple or grid) pbc = xyz rlist = 1.2 ;cut-off distance nm ; OPTIONS FOR ELECTROSTATICS coulombtype = PME ;Method for doing electrostatics rcoulomb = 1.2 ;Coulomb cut-off distance nm epsilon-r = 1.0 ;relative dielectric constant ; VDW vdw-type = Cut-off ;Method for doing VDW rvdw = 1.5 ;cut-off lengths nm ;DispCorr = EnerPres ;Apply long range dispersion corrections for Energy and Pressure fourierspacing = 0.1 ;Spacing for the PME/PPPM FFT grid ; EWALD/PME/PPPM parameters pme_order = 4 ;cubic interpolation ewald_rtol = 1e-05 ;relative Evald-shifted potential at cut-off optimize_fft = yes ;calculate at startup ; OPTIONS FOR WEAK COUPLING ALGORITHMS Tcoupl = Berendsen ;Temperature coupling Tc-grps = System ;Groups to couple separately tau_T = 5.0 ;Time constant (ps) ref_T = 299 ;reference temperature (K) Pcoupl = no ;Pressure coupling Pcoupltype = Isotropic tau_P = 5.0 ;Time constant (ps) compressibility = 4.5e-5 ;compressibility (1/bar) ref_P = 1.0 ;reference P (bar) ; OPTIONS FOR BONDS constraints = all-bonds constraint-algorithm = lincs ;shake_tol = 0.0001 unconstrained-start = yes ;don't constrain the start configuration lincs-order = 4 ;Highest order in the expansion of the constraint coupling matrix lincs-warnangle = 30 lincs-iter = 2 morse = no ;Convert harmonic bonds to morse potentials ;GENERATE VELOCITES gen_vel = no ;generates velocities gen_temp = 299 gen_seed = 173529 Could anyone help me? Thanks Egidijus Kuprusevicius Be a better friend, newshound, and know-it-all with Yahoo! Mobile. Try it now.
Re: [gmx-users] Lincs error and explosion of the system
Why don't you do energy minimization? It's pretty clear that you've generated some atomic overlap in your procedure, from what you've described. For general reference on such problems, check the hundreds of related posts (LINCS warnings) in the list archive or the following link to the wiki site: http://wiki.gromacs.org/index.php/blowing_up -Justin Quoting Egidijus Kuprusevicius [EMAIL PROTECTED]: Dear users, I have a problem on running MD of 146 LC molecules system. I do not do the energy minimisation. I use NVT ensemble to equilibrate my system. My topology was created using PRODRG beta server. After the creation of my systems box (on top of each other) 1. editconf -f lc -bt d -box 1.3 0.02 0.02 -princ -c -d 0.5 -rvdw 0.12 -o lcc 2. genconf -f lcc -nbox 8 8 8 -dist 0 0 0 -nmolat 27 -o lc512 I put inside another (a little bigger) molecule 3. editconf -f sl -bt c -box 6 -princ -c -d 2.5 -rvdw 0.12 -o sll 4. genbox -cp sll -cs lc512 -o slw -p sl then create tpr 5. grompp -v -np 32 -shuffle -sort -f eq.mdp -c slw -p sl -o topol.tpr and submit the job I always get my system exploding Initializing LINear Constraint Solver number of constraints is 122 average number of constraints coupled to one constraint is 3.0 Rel. Constraint Deviation: Max between atoms RMS Before LINCS 0.086035 40 39 0.026421 After LINCS 0.000704 103 104 0.000292 Energies (kJ/mol) G96Angle Proper Dih. Improper Dih. LJ-14 Coulomb-14 2.76783e+03 8.11377e+01 8.21662e+01 3.98602e+04 5.57164e+03 LJ (SR) LJ (LR) Coulomb (SR) Coul. recip. Potential 2.71048e+03 -1.88575e+02 -3.38992e+03 -3.62073e+04 1.12877e+04 Kinetic En. Total Energy Temperature Pressure (bar) 6.65517e+04 7.78394e+04 2.06669e+03 1.75872e+05 Step 86, time 0.172 (ps) LINCS WARNING relative constraint deviation after LINCS: max 96.909290 (between atoms 85 and 86) rms 10.933811 bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 77 78 113.7 0.1390 0.5917 0.1390 77 87 116.3 0.1390 0.5570 0.1390 78 79 109.8 0.1090 0.5917 0.1090 78 80 104.4 0.1390 1.2899 0.1390 80 81 93.6 0.1090 5.0458 0.1090 82 80 99.8 0.1390 3.9224 0.1390 82 83 100.5 0.1430 3.8921 0.1430 82 85 99.9 0.1390 3.9638 0.1390 83 84 103.4 0.1140 3.1119 0.1140 85 86 91.7 0.1090 10.6721 0.1090 85 87 100.2 0.1390 1.7797 0.1390 87 88 110.3 0.1090 0.5717 0.1090 Constraint error in algorithm Lincs at step 86 Wrote pdb files with previous and current coordinates Large VCM(group rest): -949890684120872786061526585043023133196136319944012857455888493019588547485855908650717825011817737590092000256377384500897124503083675335640562545921274578670325230339034153228858928503740516247758241500986457604229169152.0, -770017767340537250834106819849535443794415171890886583459517725651760798703652487434834859771194101005699859793685064099787214560958505758284878533509661264882479706501126070295847653568962516830194295490734095350104064.0, -17482030675841594076114066100363479435124387445824631353703195421406478322250794440904806833364056039859394683424411714469447896344546474426178109668279235955517800609185251692588873229116161214420413237478774727134943379456.0, ekin-cm: inf MDP file title = molecular dynamics cpp = /usr/bin/cpp include = -I../top ; RUN CONTROL PARAMETERS integrator = md dt = 0.002 ;ps nsteps = 500 ;10 ns ;comm_mode = Angular ;remove center of mass translation and rotation around the center of mass nstcomm = 1 ;number of steps for center of mass motion removal ; OUTPUT CONTROL OPTIONS nstxout = 100 ;every 0.2 ps nstvout = 100 nstfout = 0 nstlog = 100 ;Output frequency to write energies to log file nstenergy = 100 ;Output frequency to write energies to energy file energygrps = MMM DRG ;Selection of energy groups ; NEIGHBOR SEARCHING PARAMETERS nstlist = 1 ;update frequency ns_type = grid ;algorithm (simple or grid) pbc = xyz rlist = 1.2 ;cut-off distance nm ; OPTIONS FOR ELECTROSTATICS coulombtype = PME ;Method for doing electrostatics rcoulomb = 1.2 ;Coulomb cut-off distance nm epsilon-r = 1.0 ;relative dielectric constant ; VDW vdw-type = Cut-off ;Method for doing VDW rvdw = 1.5 ;cut-off lengths nm ;DispCorr = EnerPres ;Apply long range dispersion corrections for Energy and Pressure fourierspacing = 0.1 ;Spacing for the PME/PPPM FFT grid ; EWALD/PME/PPPM parameters pme_order = 4 ;cubic interpolation ewald_rtol = 1e-05 ;relative Evald-shifted potential at cut-off optimize_fft = yes ;calculate at startup ; OPTIONS FOR WEAK COUPLING ALGORITHMS Tcoupl = Berendsen ;Temperature coupling Tc-grps = System ;Groups to couple separately tau_T = 5.0 ;Time constant (ps) ref_T = 299 ;reference temperature (K) Pcoupl = no ;Pressure coupling Pcoupltype = Isotropic tau_P = 5.0 ;Time constant (ps) compressibility = 4.5e-5 ;compressibility (1/bar) ref_P = 1.0 ;reference P (bar) ; OPTIONS FOR BONDS constraints = all-bonds constraint-algorithm = lincs ;shake_tol
[gmx-users] LINCS error
hello users, i am using gromacs 3.3 version on unix platform i got these error while running MD simulation of 89 aa in spc216 water for 10ns at step 4088373 time 8176.55 .i had used force field 4a1(official distribution) hear I'm sending .mdp file also error which i got is -- step 4088520, will finish at Sat Sep 22 06:22:35 2007 Step 4088530, time 8177.06 (ps) LINCS WARNING relative constraint deviation after LINCS: max 17.051964 (between atoms 615 and 616) rms 0.709711 bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 613614 35.70.1233 0.1232 0.1230 613615 35.20.1332 0.1352 0.1330 615616 90.00.0997 1.8052 0.1000 615617 90.00.1322 1.3965 0.1000 step 4088530, will finish at Sat Sep 22 06:22:35 2007Warning: 1-4 interaction at distance larger than 1 These are ignored for the rest of the simulation turn on -debug for more information Step 4088531, time 8177.06 (ps) LINCS WARNING relative constraint deviation after LINCS: max 1.625723 (between atoms 615 and 617) rms 0.062578 bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 612613 46.40.1548 0.1344 0.1530 613614 37.20.1232 0.1816 0.1230 613615 89.70.1352 0.2216 0.1330 615616 76.31.8052 0.1476 0.1000 615617 89.71.3965 0.2626 0.1000 Step 4088532, time 8177.06 (ps) LINCS WARNING relative constraint deviation after LINCS: max 14.399930 (between atoms 615 and 616) rms 0.598937 bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 611612 44.20.1693 0.1761 0.1530 612613 35.40.1344 0.1669 0.1530 613614 95.70.1816 0.1308 0.1230 615616 90.20.1476 1.5400 0.1000 615617 90.50.2626 1.1927 0.1000 Step 4088533, time 8177.07 (ps) LINCS WARNING relative constraint deviation after LINCS: max 1.051080 (between atoms 615 and 617) rms 0.046065 bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 609611 44.50.1529 0.1910 0.1470 611612 39.90.1761 0.1800 0.1530 611618 41.90.1579 0.1736 0.1530 612613 105.90.1669 0.2124 0.1530 613614 123.80.1308 0.1181 0.1230 613615 34.60.1178 0.2224 0.1330 615616 74.01.5400 0.1253 0.1000 615617 80.31.1927 0.2051 0.1000 Step 4088534, time 8177.07 (ps) LINCS WARNING relative constraint deviation after LINCS: max 45040.144531 (between atoms 613 and 614) rms 1994.670654 bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 582584 41.90.1470 0.2116 0.1470 584585 41.30.1530 0.2102 0.1530 584586 69.20.1530 8.3830 0.1530 586587 59.20.1230 8.3382 0.1230 586588 78.90.1331 28.5889 0.1330 588589 75.70.1001 27.4635 0.1000 588590 80.70.1471 156.4029 0.1470 590591 82.50.1531 156.2125 0.1530 590607 84.10.1537 272.5951 0.1530 591592 78.30.1531 23.8232 0.1530 592593 55.20.1330 6.7518 0.1330 592595 55.70.1390 6.7401 0.1390 593594 41.60.1090 0.1595 0.1090 593596 45.10.1330 0.1971 0.1330 595598 37.70.1390 0.1911 0.1390 595599 34.40.1390 0.1923 0.1390 607608 85.10.1235 322.3230 0.1230 607609 90.80.1334 722.2238 0.1330 609610 87.50.1001 730.5731 0.1000 609611 91.70.1910 2220.5916 0.1470 611612 113.10.1800 1928.0201 0.1530 611618 61.90.1736 2612.3730 0.1530 612613 152.60.2124 2170.9067 0.1530 613614 95.00.1181 5540.0610 0.1230 613615 100.80.2224 1264.8948 0.1330 615616 88.00.1253 729.0342 0.1000 615617 69.10.2051 610.1647 0.1000 618619 96.00.1365 1772.1053 0.1230 618620 101.80.1456 1954.0292 0.1330 620621 97.10.1014 161.6277 0.1000 620622 44.00.1484 387.2649 0.1470 622623 119.20.1536 271.5126 0.1530 622628 110.20.1536 303.3078 0.1530 623624 65.60.1531 51.2406 0.1530 624625 113.70.1530 26.6845 0.1530 625626 32.70.1250 0.1557 0.1250 625627 34.20.1250 0.1577
Re: [gmx-users] LINCS error
This is an issue that has been discussed a lot on the list. The typical reasons for LINCS errors can be found here: http://wiki.gromacs.org/index.php/Errors#LINCS_warnings Quoting vijay kumar hinge vijay [EMAIL PROTECTED]: hello users, i am using gromacs 3.3 version on unix platform i got these error while running MD simulation of 89 aa in spc216 water for 10ns at step 4088373 time 8176.55 .i had used force field 4a1(official distribution) hear I'm sending .mdp file also error which i got is ; Berendsen temperature coupling is on in two groups Tcoupl = berendsen tc-grps = Protein SOL NA+ tau_t = 0.1 0.1 0.1 ref_t = 300300 300 Also note that this is a bad idea - never couple solvent and ions separately. Make an index group with both components merged into one group. -Justin == Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA [EMAIL PROTECTED] | (540) 231-9080 http://bevanlab.biochem.vt.edu/Pages/Personal/justin/ == ___ gmx-users mailing listgmx-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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] LINCS error during mdrun
Mark Abraham a écrit : Dear GROMACS users, I am trying to run md of a protein with a non-standard residue. It was fine up until I ran mdrun with pr.mdp, where I received a LINCS warning after 20 steps (0.042 ps). Step 21, time 0.042 (ps) LINCS WARNING I looked up the mailing list and found discussion about this subject but there appears to be no conclusions. That's because the problem lies with your topology or your structure. Have a look at the structures and see what is wrong. Either you need to fix the topology, or you haven't relaxed a bad atomic contact enough. I wish I had a dollar for every time I've given the above advice for a LINCS error! Mark Set up a donation page :-) -- Stéphane Téletchéa, PhD. http://www.steletch.org Unité Mathématique Informatique et Génome http://migale.jouy.inra.fr/mig INRA, Domaine de Vilvert Tél : (33) 134 652 891 78352 Jouy-en-Josas cedex, France Fax : (33) 134 652 901 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] LINCS error during mdrun
Dear GROMACS users, I am trying to run md of a protein with a non-standard residue. It was fine up until I ran mdrun with pr.mdp, where I received a LINCS warning after 20 steps (0.042 ps). Step 21, time 0.042 (ps) LINCS WARNING I looked up the mailing list and found discussion about this subject but there appears to be no conclusions. That's because the problem lies with your topology or your structure. Have a look at the structures and see what is wrong. Either you need to fix the topology, or you haven't relaxed a bad atomic contact enough. I wish I had a dollar for every time I've given the above advice for a LINCS error! Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] LINCS error during mdrun
Hi Shangwa Han, First of all, there is no general conclusion regarding such error. Second, the general conclusion is: your system contains severe errors, which have not been resolved during energy minimization, if you performed any, but you didn't mention it. If you would have browsed the archive more thoroughly or had read the posts of the last days, regarding non-standard residues, you would have noticed that the problem has been met before. Now, first of all, what residue do you have? Did you perform energy minimization (vacuum and/or solvated)? Did energy minimization converge? Did the potential energy after energy minimization seem reasonable (well negative)? What atoms are causing the failure? I have no idea to what the atom numbers correspond... Maybe it's good to have read the following (and taking the advice) when asking a question on this (or any) list: http://catb.org/esr/faqs/smart-questions.html Tsjerk On 1/25/07, 한상화 [EMAIL PROTECTED] wrote: Dear GROMACS users, I am trying to run md of a protein with a non-standard residue. It was fine up until I ran mdrun with pr.mdp, where I received a LINCS warning after 20 steps (0.042 ps). Step 21, time 0.042 (ps) LINCS WARNING relative constraint deviation after LINCS: max 236965036032.00 (between atoms 261 and 262) rms 7344678400.00 bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 250252 70.20.1331 0.0388 0.1330 252253 133.70.1000 0.1070 0.1000 252254 113.70.1471 584679.3560 0.1470 254255 99.10.1531 4371462.3199 0.1530 254268 113.20.1531 584679.3412 0.1530 255256 104.00.1531 14918575.9155 0.1530 256257 94.10.1391 71642892.3147 0.1390 256259 118.90.1391 9989150.8212 0.1390 257258 94.70.1090 53680649.8250 0.1090 257261 92.00.1391 165281594.0708 0.1390 259260 167.30.1090 3058365.4015 0.1090 259263 102.70.1391 23632615.9567 0.1390 261262 90.00.1090 25829189100.6878 0.1090 261265 93.50.1391 151539192.8914 0.1390 263264 102.70.1090 23369011.4797 0.1090 263265 99.00.1391 51420376.9215 0.1390 265266 96.00.1361 61029666.4858 0.1360 266267 93.30.1000 22670607.4602 0.1000 268269 123.50.1230 0.1132 0.1230 268270 89.00.1331 0.0916 0.1330 270271 32.20.1000 0.1280 0.1000 270272 32.30.1471 0.1820 0.1470 I looked up the mailing list and found discussion about this subject but there appears to be no conclusions. Any suggestions would be greatly appreciated. Sanghwa Han ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] LINCS error during mdrun
Dear GROMACS users, I am trying to run md of a protein with a non-standard residue. It was fine up until I ran mdrun with pr.mdp, where I received a LINCS warning after 20 steps (0.042 ps). Step 21, time 0.042 (ps) LINCS WARNING relative constraint deviation after LINCS: max 236965036032.00 (between atoms 261 and 262) rms 7344678400.00 bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 250252 70.20.1331 0.0388 0.1330 252253 133.70.1000 0.1070 0.1000 252254 113.70.1471 584679.3560 0.1470 254255 99.10.1531 4371462.3199 0.1530 254268 113.20.1531 584679.3412 0.1530 255256 104.00.1531 14918575.9155 0.1530 256257 94.10.1391 71642892.3147 0.1390 256259 118.90.1391 9989150.8212 0.1390 257258 94.70.1090 53680649.8250 0.1090 257261 92.00.1391 165281594.0708 0.1390 259260 167.30.1090 3058365.4015 0.1090 259263 102.70.1391 23632615.9567 0.1390 261262 90.00.1090 25829189100.6878 0.1090 261265 93.50.1391 151539192.8914 0.1390 263264 102.70.1090 23369011.4797 0.1090 263265 99.00.1391 51420376.9215 0.1390 265266 96.00.1361 61029666.4858 0.1360 266267 93.30.1000 22670607.4602 0.1000 268269 123.50.1230 0.1132 0.1230 268270 89.00.1331 0.0916 0.1330 270271 32.20.1000 0.1280 0.1000 270272 32.30.1471 0.1820 0.1470 I looked up the mailing list and found discussion about this subject but there appears to be no conclusions. Any suggestions would be greatly appreciated. Sanghwa Han ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] lincs error
Hi! this is my problem: after a few step (from 1 to 20) mdrun stops because of lincs ...LINCS WARNING - Relative constraint deviation after lincs: max 103.684275 (between atoms 7941 and 7942) rms 1.227871 bonds that rotated more than 180 degrees... 7941 e 7942 should be two water atoms. There are more than one WARNING If I use a smaller time step (1fs instead of 4 fs or 2 fs) there is no problem, and it works well! What can I do? Beniamino ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] LINCS Error in Gromacs-3.3.1 in pr simulation
Dear all, I have been trying to simulate various mutant models (single mutant) of a enzyme. I am successfully finished simulation of 3 variants including wild type (So for finished up to position restraints of all variants). In one mutation involving Ala in requsite position happened to be unfinished at the stage of position restraint. The error is of old kind , which I have pasted below. I am surprised about the fact that all system of almost simillar execpt one mutant residues went through undisturbed but this particular varient creating problem. I used same parameter files without any change for all simulation. More to add for your information, I am simulating all protein with bound ligand molecules. The Error is pasted below # Step 142, time 0.284 (ps) LINCS WARNING relative constraint deviation after LINCS: max 6425310107478786048.00 (between atoms 1266 and 1267) rms NaN bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 1232 1234 45.20.1449 0.2169 0.1449 1234 1235 48.40.1090 0.1784 0.1090 1234 1236 44.70.1529 0.2261 0.1529 1234 1249 122.50.1522 136533780725760. 0.1522 1249 1250 119.00.1229 136533780725760. 0.1229 1249 1251 109.10.1335 603724024119296. 0.1335 1251 1252 108.90.1010 586193511120896. 0.1010 1251 1253 100.60.1449 3357735101923328. 0.1449 1253 1254 98.00.1090 3204054192750592. 0.1090 1253 1255 97.40.1529 3419750134710272. 0.1529 1253 1264 97.60.1522 9328680778072064. 0.1522 1255 1256 102.10.1090 516437605089280. 0.1090 1255 1257 103.20.1090 510584571297792. 0.1090 1255 1258 100.10.1529 531077537988608. 0.1529 1258 1259 110.20.1090 46668405800960. 0.1090 1258 1260 115.10.1090 46668405800960. 0.1090 1258 1261 111.30.1522 46668405800960. 0.1522 1264 1265 96.80.1229 8772496471883776. 0.1229 1264 1266 93.40.1335 23058375889649664. 0.1335 1266 1267 90.10.1010 648956295566589952. 0.1010 1266 1268 92.80.1449 20309538838151168. 0.1449 1268 1269 93.70.1090 9442003490177024. 0.1090 1268 1270 94.10.1529 10569273491587072. 0.1529 1268 1275 94.60.1522 10709468740321280. 0.1522 1270 1271 97.40.1090 2281559910514688. 0.1090 1270 1272 96.70.1090 2346805832450048. 0.1090 1270 1273 97.60.1410 2468801157267456. 0.1410 1273 1274 98.10.0945 516787946913792. 0.0945 1275 1276 103.00.1229 1965350593757184. 0.1229 1275 1277 105.20.1335 1981484369969152. 0.1335 1277 1278 112.00.1010 484401947344896. 0.1010 1277 1279 105.50.1449 537563274149888. 0.1449 1279 1280 114.60.1090 93084121563136. 0.1090 1279 1281 107.40.1529 93082670333952. 0.1529 1279 1290 106.90.1522 93082821328896. 0.1522 1281 1282 83.50.1090 1272794624. 0.1090 1281 1283 85.00.1090 1321838592. 0.1090 1281 1284 82.10.1529 1407034368. 0.1529 1284 1285 85.90.1090 283390016. 0.1090 1284 1286 84.90.1090 264245008. 0.1090 1284 1287 88.20.1522 295514624. 0.1522 1287 1288 55.50.1250 47520624. 0.1250 1287 1289 66.60.1250 47520412. 0.1250 1290 1291 74.90.1229 1078725504. 0.1229 1290 1292 76.20.1335 1155043328. 0.1335 1292 1293 72.90.1010 250017072. 0.1010 1292 1294 78.60.1449 282246560. 0.1449 1294 1295 69.00.1090 79070984. 0.1090 1294 1296 63.80.1529 79075408. 0.1529 1294 1301 71.90.1522 79078832. 0.1522 1296 1297 79.50.1090 18558.5371 0.1090 1296 1298 82.70.1090 19417.0156 0.1090 1296 1299 79.40.1410 19846.6992 0.1410 1299 1300 88.40.0945 2605.6270 0.0945 1301 1302 78.30.1229 17848.5957 0.1229 1301 1303 72.30.1335 17940.1172 0.1335 1303 1304 72.90.1010 4016.1282 0.1010 1303 1305 77.50.1449 4398.8486 0.1449 1305 1306 79.00.1090 1363.8757 0.1090 1305 1307 66.20.1529 1353.4260 0.1529 1305 1315 72.90.1522 1368.8561 0.1522 $ 1307 1309 121.40.1410 25.7220 0.1410 1307 1311 142.80.1529
