Re: [gmx-users] LINCS WARNING - Protein-Membrane-system
On 1/1/13 8:56 AM, Shima Arasteh wrote: Hi, I have a system of Peptide-popc-ions-water to simulate. I'm trying to run MD simulation following the Justin's tutorial of kalp15-DPPC. The force field which I use, is charmm36. In NVT step, I get LINCS-warning as follow: Step 0, time 0 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 2.460224, max 54.696251 (between atoms 4719 and 4716) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length Step 0, time 0 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.182707, max 15.613569 (between atoms 4725 and 4726) When I checked the warning, I see the first warning is related to 2 atoms of 71POPC, the chain of 71POPC residue is broken near these two atoms. And the other warning is related to a bond between H and C in the other POPC residue. Some settings of nvt.mdp is as: ns_type= grid nstlist= 5 rlist= 1.2 rlistlong = 1.4 rcoulomb= 1.2 rvdw= 1.2 pbc= xyz vdwtype = switch rvdw_switch = 0.8 ; Parameters for treating bonded interactions continuation= no constraint_algorithm = LINCS constraints= all-bonds lincs_iter= 1 lincs_order= 4 Do I need to increase the rlistlong? I have done a simulation of POPC-water before with these settings, but everything was ok. So what's the problem? Anybody may help me? Don't haphazardly mess with cutoffs. Doing so usually makes your problem worse. Think about it scientifically - if POPC/water worked fine, but a POPC/protein/water system doesn't, what's the variable that changed? Moreover, look at when the failure is happening - it's failing at step zero. LINCS warnings always have the same causes: 1. Wrong .mdp settings (likely not the case, see above) 2. Insufficient equilibration (well, yours is failing outright, so probably not) 3. Insufficient minimization (hmmm...) -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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
Re: [gmx-users] LINCS WARNING - Protein-Membrane-system
Thanks. I compared settings of mdp files in POPC/WATER and POPC/PROTEIN/WATER systems. The only difference I found between them was about the bonds constraints. The constraints of mdp file for POPC/WATER was constraints = h-bonds , however it was constraints = all-bonds for POPC/PROTEIN/WATER system. You say insufficient minimization, I don't think so . I got a sensible potential energy as follow: Potential Energy = -1.2414742e+06 Maximum force = 9.8055229e+01 on atom 4719 Norm of force = 3.4904923e+00 Then what's wrong with the EM? Sincerely, Shima - Original Message - From: Justin Lemkul jalem...@vt.edu To: Shima Arasteh shima_arasteh2...@yahoo.com; Discussion list for GROMACS users gmx-users@gromacs.org Cc: Sent: Tuesday, January 1, 2013 6:45 PM Subject: Re: [gmx-users] LINCS WARNING - Protein-Membrane-system On 1/1/13 8:56 AM, Shima Arasteh wrote: Hi, I have a system of Peptide-popc-ions-water to simulate. I'm trying to run MD simulation following the Justin's tutorial of kalp15-DPPC. The force field which I use, is charmm36. In NVT step, I get LINCS-warning as follow: Step 0, time 0 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 2.460224, max 54.696251 (between atoms 4719 and 4716) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length Step 0, time 0 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.182707, max 15.613569 (between atoms 4725 and 4726) When I checked the warning, I see the first warning is related to 2 atoms of 71POPC, the chain of 71POPC residue is broken near these two atoms. And the other warning is related to a bond between H and C in the other POPC residue. Some settings of nvt.mdp is as: ns_type = grid nstlist = 5 rlist = 1.2 rlistlong = 1.4 rcoulomb = 1.2 rvdw = 1.2 pbc = xyz vdwtype = switch rvdw_switch = 0.8 ; Parameters for treating bonded interactions continuation = no constraint_algorithm = LINCS constraints = all-bonds lincs_iter = 1 lincs_order = 4 Do I need to increase the rlistlong? I have done a simulation of POPC-water before with these settings, but everything was ok. So what's the problem? Anybody may help me? Don't haphazardly mess with cutoffs. Doing so usually makes your problem worse. Think about it scientifically - if POPC/water worked fine, but a POPC/protein/water system doesn't, what's the variable that changed? Moreover, look at when the failure is happening - it's failing at step zero. LINCS warnings always have the same causes: 1. Wrong .mdp settings (likely not the case, see above) 2. Insufficient equilibration (well, yours is failing outright, so probably not) 3. Insufficient minimization (hmmm...) -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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
Re: [gmx-users] LINCS WARNING - Protein-Membrane-system
On 1/1/13 10:41 AM, Shima Arasteh wrote: Thanks. I compared settings of mdp files in POPC/WATER and POPC/PROTEIN/WATER systems. The only difference I found between them was about the bonds constraints. The constraints of mdp file for POPC/WATER was constraints = h-bonds , however it was constraints = all-bonds for POPC/PROTEIN/WATER system. You say insufficient minimization, I don't think so . I got a sensible potential energy as follow: Potential Energy = -1.2414742e+06 Maximum force = 9.8055229e+01 on atom 4719 Norm of force = 3.4904923e+00 Then what's wrong with the EM? Please post a complete .mdp file for both the EM and NVT processes. Without that information, it's pure guesswork. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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
Re: [gmx-users] LINCS WARNING - Protein-Membrane-system
Lemkul jalem...@vt.edu To: Discussion list for GROMACS users gmx-users@gromacs.org Cc: Sent: Tuesday, January 1, 2013 7:17 PM Subject: Re: [gmx-users] LINCS WARNING - Protein-Membrane-system On 1/1/13 10:41 AM, Shima Arasteh wrote: Thanks. I compared settings of mdp files in POPC/WATER and POPC/PROTEIN/WATER systems. The only difference I found between them was about the bonds constraints. The constraints of mdp file for POPC/WATER was constraints = h-bonds , however it was constraints = all-bonds for POPC/PROTEIN/WATER system. You say insufficient minimization, I don't think so . I got a sensible potential energy as follow: Potential Energy = -1.2414742e+06 Maximum force = 9.8055229e+01 on atom 4719 Norm of force = 3.4904923e+00 Then what's wrong with the EM? Please post a complete .mdp file for both the EM and NVT processes. Without that information, it's pure guesswork. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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 -- 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 WARNING - Protein-Membrane-system
On 1/1/13 10:53 AM, Shima Arasteh wrote: If I tell you that I changed the constraints and now the NVT is running, would that be ok? However I don't know the scientific reason of this incident! But I bring you the EM.mdp as follow: define = -DSTRONG_POSRES integrator= steep; Algorithm (steep = steepest descent minimization) emtol= 100.0 ; Stop minimization when the maximum force 100.0 kJ/mol/nm emstep= 0.01 ; Energy step size nsteps= 5 ; Maximum number of (minimization) steps to perform ; Parameters describing how to find the neighbors of each atom and how to calculate the interactions nstlist= 1; Frequency to update the neighbor list and long range forces ns_type= grid; Method to determine neighbor list (simple, grid) rlist= 1.2; Cut-off for making neighbor list (short range forces) coulombtype= PME; Treatment of long range electrostatic interactions rcoulomb= 1.2; Short-range electrostatic cut-off rvdw= 1.2; Short-range Van der Waals cut-off pbc= xyz ; Periodic Boundary Conditions And the NVT.mdp as follow (after change of all-bond constraint to h-bond): title= NVT equilibration for dimer-POPC - CHARMM36 define= -DPOSRES; Protein is position restrained (uses the posres.itp file information) ; Parameters describing the details of the NVT simulation protocol integrator= md; Algorithm (md = molecular dynamics [leap-frog integrator]; md-vv = md using velocity verlet; sd = stochastic dynamics) dt= 0.002; Time-step (ps) nsteps= 5; Number of steps to run (0.002 * 5 = 100 ps) ; Parameters controlling output writing nstxout= 1; Write coordinates to output .trr file every 2 ps nstvout= 1000; Write velocities to output .trr file every 2 ps nstenergy= 1000; Write energies to output .edr file every 2 ps nstlog= 1000; Write output to .log file every 2 ps ; Parameters describing neighbors searching and details about interaction calculations ns_type= grid; Neighbor list search method (simple, grid) nstlist= 5; Neighbor list update frequency (after every given number of steps) rlist= 1.2; Neighbor list search cut-off distance (nm) rlistlong = 1.4 rcoulomb= 1.2; Short-range Coulombic interactions cut-off distance (nm) rvdw= 1.2; Short-range van der Waals cutoff distance (nm) pbc= xyz; Direction in which to use Perodic Boundary Conditions (xyz, xy, no) vdwtype = switch rvdw_switch = 0.8 ; Parameters for treating bonded interactions continuation= no; Whether a fresh start or a continuation from a previous run (yes/no) constraint_algorithm = LINCS; Constraint algorithm (LINCS / SHAKE) constraints= h-bonds ; Which bonds/angles to constrain (all-bonds / hbonds / none / all-angles / h-angles) lincs_iter= 1; Number of iterations to correct for rotational lengthening in LINCS (related to accuracy) lincs_order= 4; Highest order in the expansion of the constraint coupling matrix (related to accuracy) ; Parameters for treating electrostatic interactions coulombtype= PME; Long range electrostatic interactions treatment (cut-off, Ewald, PME) pme_order= 4; Interpolation order for PME (cubic interpolation is represented by 4) fourierspacing= 0.16; Maximum grid spacing for FFT grid using PME (nm) ; Temperature coupling parameters tcoupl= v-rescale; Modified Berendsen thermostat using velocity rescaling tc-grps= Protein POPCSOL_CL; Define groups to be coupled separately to temperature bath tau_t= 0.10.10.1; Group-wise coupling time constant (ps) ref_t= 310 310310; Group-wise reference temperature (K) ; Pressure coupling parameters pcoupl= no ; Under NVT conditions pressure coupling is not done ; Miscellaneous control parameters ; Dispersion correction DispCorr= EnerPres; Dispersion corrections for Energy and Pressure for vdW cut-off ; Initial Velocity Generation gen_vel= yes; Generate velocities from Maxwell distribution at given temperature gen_temp= 310; Specific temperature for Maxwell distribution (K) gen_seed= -1; Use random seed for velocity generation (integer; -1 means seed is calculated from the process ID number) ; Centre of mass (COM) motion removal relative to the specified groups nstcomm= 1; COM removal frequency (steps) comm_mode= Linear; Remove COM translation (linear / angular / no) comm_grps= Protein_POPC SOL_CL; COM removal relative to the specified groups Any suggestions please? Yes, the
Re: [gmx-users] LINCS WARNING - Protein-Membrane-system
Thanks. Sincerely, Shima - Original Message - From: Justin Lemkul jalem...@vt.edu To: Shima Arasteh shima_arasteh2...@yahoo.com; Discussion list for GROMACS users gmx-users@gromacs.org Cc: Sent: Tuesday, January 1, 2013 7:27 PM Subject: Re: [gmx-users] LINCS WARNING - Protein-Membrane-system On 1/1/13 10:53 AM, Shima Arasteh wrote: If I tell you that I changed the constraints and now the NVT is running, would that be ok? However I don't know the scientific reason of this incident! But I bring you the EM.mdp as follow: define = -DSTRONG_POSRES integrator = steep ; Algorithm (steep = steepest descent minimization) emtol = 100.0 ; Stop minimization when the maximum force 100.0 kJ/mol/nm emstep = 0.01 ; Energy step size nsteps = 5 ; Maximum number of (minimization) steps to perform ; Parameters describing how to find the neighbors of each atom and how to calculate the interactions nstlist = 1 ; Frequency to update the neighbor list and long range forces ns_type = grid ; Method to determine neighbor list (simple, grid) rlist = 1.2 ; Cut-off for making neighbor list (short range forces) coulombtype = PME ; Treatment of long range electrostatic interactions rcoulomb = 1.2 ; Short-range electrostatic cut-off rvdw = 1.2 ; Short-range Van der Waals cut-off pbc = xyz ; Periodic Boundary Conditions And the NVT.mdp as follow (after change of all-bond constraint to h-bond): title = NVT equilibration for dimer-POPC - CHARMM36 define = -DPOSRES ; Protein is position restrained (uses the posres.itp file information) ; Parameters describing the details of the NVT simulation protocol integrator = md ; Algorithm (md = molecular dynamics [leap-frog integrator]; md-vv = md using velocity verlet; sd = stochastic dynamics) dt = 0.002 ; Time-step (ps) nsteps = 5 ; Number of steps to run (0.002 * 5 = 100 ps) ; Parameters controlling output writing nstxout = 1 ; Write coordinates to output .trr file every 2 ps nstvout = 1000 ; Write velocities to output .trr file every 2 ps nstenergy = 1000 ; Write energies to output .edr file every 2 ps nstlog = 1000 ; Write output to .log file every 2 ps ; Parameters describing neighbors searching and details about interaction calculations ns_type = grid ; Neighbor list search method (simple, grid) nstlist = 5 ; Neighbor list update frequency (after every given number of steps) rlist = 1.2 ; Neighbor list search cut-off distance (nm) rlistlong = 1.4 rcoulomb = 1.2 ; Short-range Coulombic interactions cut-off distance (nm) rvdw = 1.2 ; Short-range van der Waals cutoff distance (nm) pbc = xyz ; Direction in which to use Perodic Boundary Conditions (xyz, xy, no) vdwtype = switch rvdw_switch = 0.8 ; Parameters for treating bonded interactions continuation = no ; Whether a fresh start or a continuation from a previous run (yes/no) constraint_algorithm = LINCS ; Constraint algorithm (LINCS / SHAKE) constraints = h-bonds ; Which bonds/angles to constrain (all-bonds / hbonds / none / all-angles / h-angles) lincs_iter = 1 ; Number of iterations to correct for rotational lengthening in LINCS (related to accuracy) lincs_order = 4 ; Highest order in the expansion of the constraint coupling matrix (related to accuracy) ; Parameters for treating electrostatic interactions coulombtype = PME ; Long range electrostatic interactions treatment (cut-off, Ewald, PME) pme_order = 4 ; Interpolation order for PME (cubic interpolation is represented by 4) fourierspacing = 0.16 ; Maximum grid spacing for FFT grid using PME (nm) ; Temperature coupling parameters tcoupl = v-rescale ; Modified Berendsen thermostat using velocity rescaling tc-grps = Protein POPC SOL_CL ; Define groups to be coupled separately to temperature bath tau_t = 0.1 0.1 0.1 ; Group-wise coupling time constant (ps) ref_t = 310 310 310 ; Group-wise reference temperature (K) ; Pressure coupling parameters pcoupl = no ; Under NVT conditions pressure coupling is not done ; Miscellaneous control parameters ; Dispersion correction DispCorr = EnerPres ; Dispersion corrections for Energy and Pressure for vdW cut-off ; Initial Velocity Generation gen_vel = yes ; Generate velocities from Maxwell distribution at given temperature gen_temp = 310 ; Specific temperature for Maxwell distribution (K) gen_seed = -1 ; Use random seed for velocity generation
Re: [gmx-users] LINCS WARNING relative constraint deviation
On 10/1/12 7:10 AM, Ali Alizadeh wrote: Dear all users 1- I am trying to simulate a system that contains 1182 methane molecules(5910 atoms) and 1830 water molecules(5490), I keep getting these errors. Something is wrong with the starting configuration, topology, or .mdp settings (see below for comments) such that energy minimization fails almost instantly. http://www.gromacs.org/Documentation/Terminology/Blowing_Up 2- Gromacs does not give me a .xtc file, Why? Perhaps there's some quirk of the code that won't produce an .xtc file with an EM algorithm. EM is normally quick and takes up little disk space, so the benefit to having a compressed trajectory is minimal in most cases. My command lines for grompp and mdrun in terminal window: grompp -f npt.mdp -c wwfull.top.gro -p topol.top -o topol.tpr -n ww.ndx mdrun -s topol.tpr -o wwfull.trr -x wwfull.xtc These are errors and my .mdp file: ... Steepest Descents: Tolerance (Fmax) = 1.0e-04 Number of steps= 1000 Step 50, time 0.01 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.000589, max 0.014000 (between atoms 2636 and 2638) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 2636 2637 39.40.1090 0.1092 0.1090 Step 51, time 0.0102 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.001802, max 0.029832 (between atoms 2026 and 2029) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 2331 2334 43.10.1090 0.1093 0.1090 2026 2028 49.60.1090 0.1095 0.1090 5071 5074 41.70.1090 0.1093 0.1090 4806 4808 47.00.1090 0.1095 0.1090 Step 52, time 0.0104 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.003002, max 0.049492 (between atoms 156 and 159) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 471474 51.70.1090 0.1096 0.1090 2331 2334 32.40.1093 0.1078 0.1090 5071 5074 31.30.1093 0.1081 0.1090 156160 55.30.1090 0.1095 0.1090 916919 41.00.1090 0.1093 0.1090 5886 5890 61.10.1090 0.1092 0.1090 Step 53, time 0.0106 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.034606, max 0.843079 (between atoms 5886 and 5890) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 471475 31.50.1049 0.1325 0.1090 471474 92.90.1096 0.1519 0.1090 471473 38.60.1044 0.1402 0.1090 471472 92.70.1048 0.1568 0.1090 2331 2335 48.80.1082 0.1083 0.1090 2331 2334 48.40.1078 0.1070 0.1090 2331 2333 88.80.1110 0.1564 0.1090 2331 2332 88.80.1110 0.1586 0.1090 2026 2030 89.40.1103 0.1177 0.1090 2026 2028 40.00.1091 0.1191 0.1090 2026 2027 38.20.1089 0.1207 0.1090 5071 5075 41.90.1084 0.1048 0.1090 5071 5074 41.60.1081 0.1043 0.1090 5071 5073 88.60.1109 0.1376 0.1090 5071 5072 88.70.1110 0.1392 0.1090 4806 4810 89.30.1104 0.1176 0.1090 4806 4809 32.70.1104 0.0927 0.1090 4806 4808 35.20.1089 0.1140 0.1090 4806 4807 35.00.1088 0.1153 0.1090 156160 92.70.1095 0.1324 0.1090 156159 80.80.1036 0.0523 0.1090 156158 90.00.1036 0.1338 0.1090 156157 90.40.1037 0.1489 0.1090 2276 2280 38.30.1091 0.1114 0.1090 2276 2277 33.00.1089 0.1134 0.1090 2286 2290 37.80.1090 0.1102 0.1090 916920 90.10.1068 0.1704 0.1090 916919 45.90.1093 0.1237 0.1090 916917 65.00.1067 0.1285 0.1090 1296 1300 31.20.1090 0.1094 0.1090 5886 5890 90.90.1092 0.2009 0.1090 5886 5889 47.90.1043 0.1326 0.1090 5886 5888 85.90.1045 0.1282 0.1090 5886 5887 91.40.1046 0.1208 0.1090 Back Off! I just backed up step53b_n0.pdb to ./#step53b_n0.pdb.1# Back Off! I just backed up step53c_n0.pdb to ./#step53c_n0.pdb.1# Wrote pdb files with previous and current coordinates .. .. .. This is my .mdp file: title= Yo cpp = /usr/bin/cpp include = define = ; RUN CONTROL PARAMETERS integrator = steep ; Start time and timestep in ps tinit= 0 dt = 0.0002 nsteps = 1000 ;
Re: [gmx-users] LINCS warning in md run
Hi, now I tried it without any restriction and still the LINCS warnings occur. Since it is always the hydrogen atom where the huge force lies on I had the idea just to remove the hydrogen atom to find out whether another atom will occur to have such a high force on or everything went fine. And indeed, without the hydrogen atom there is no problem during the MD run. Even when I fix all the other atoms. I can not see why this occurs. I already looked at the residue with pymol and I could see that there is no other residue or atom clashing with it. The residue looks like this: ATOM955 N TYP65 27.310 23.150 27.670 1.00 0.00 N ATOM956 CA TYP65 26.870 23.320 26.300 1.00 0.00 C ATOM957 C TYP65 27.920 23.760 25.300 1.00 0.00 C ATOM958 O TYP65 28.060 23.210 24.210 1.00 0.00 O ATOM959 CB TYP65 25.740 24.340 26.170 1.00 0.00 C ATOM960 CG TYP65 24.530 23.740 26.830 1.00 0.00 C ATOM961 CD1 TYP65 24.410 23.760 28.220 1.00 0.00 C ATOM962 CD2 TYP65 23.510 23.180 26.050 1.00 0.00 C ATOM963 CE1 TYP65 23.290 23.210 28.840 1.00 0.00 C ATOM964 CE2 TYP65 22.380 22.630 26.660 1.00 0.00 C ATOM965 CZ TYP65 22.260 22.630 28.070 1.00 0.00 C ATOM966 OH TYP65 21.160 22.100 28.670 1.00 0.00 O ATOM967 P TYP65 20.298 21.422 27.722 1.00 0.00 P ATOM968 OP1 TYP65 21.003 21.245 26.467 1.00 0.00 O ATOM969 OP2 TYP65 19.920 20.126 28.251 1.00 0.00 O ATOM970 OP3 TYP65 19.106 22.218 27.498 1.00 0.00 O ATOM971 H TYP65 27.210 23.914 28.325 1.00 0.00 H ATOM972 HA TYP65 26.485 22.366 25.933 1.00 0.00 H ATOM973 HB1 TYP65 25.524 24.543 25.119 1.00 0.00 H ATOM974 HB2 TYP65 26.010 25.270 26.669 1.00 0.00 H ATOM975 HD1 TYP65 25.154 24.234 28.821 1.00 0.00 H ATOM976 HD2 TYP65 23.603 23.156 24.973 1.00 0.00 H ATOM977 HE1 TYP65 23.200 23.222 29.916 1.00 0.00 H ATOM978 HE2 TYP65 21.603 22.189 26.053 1.00 0.00 H ATOM979 H1P TYP65 20.357 20.996 25.802 1.00 0.00 H The topology entry in the aminoacid.rtp file looks like this: [ TYP ] [ atoms ] NN -0.5163001 CACT 0.2755032 HAH1 0.0082233 CBCT -0.3540524 HB1HC 0.1103265 HB2HC 0.1103266 CGCA 0.1197287 CD1CA -0.1989388 HD1HA 0.1371439 CE1CA -0.284884 10 HE1HA 0.177179 11 CZC0.452616 12 OHOS -0.534452 13 HH0.293600 14 CE2CA -0.284884 15 HE2HA 0.177179 16 CD2CA -0.198938 17 HD2HA 0.137143 18 CC0.536600 19 OO -0.581900 20 PP1.393213 21 OP1OH -0.752821 22 OP2O2 -0.822464 23 OP3O2 -0.822464 24 H1PHO 0.423316 25 [ bonds ] N H NCA CAHA CACB CA C CB HB1 CB HB2 CBCG CG CD1 CG CD2 CD1 HD1 CD1 CE1 CE1 HE1 CE1CZ CZOS CZ CE2 OS P CE2 HE2 CE2 CD2 CD2 HD2 C O -C N P OP1 P OP2 P OP3 H1P OP1 [ impropers ] -CCA N H CA+N C O CG CE2 CD2 HD2 CZ CD2 CE2 HE2 CD1CZ CE1 HE1 CG CE1 CD1 HD1 CD1 CD2CGCB CE1 CE2CZOH The LINCS problems lie between the oxygen atom of the phosphate where a hydrogen atom is bound to (OP1) and the hydrogen atom bound to the oxygen atom of the phosphate (H1P). Do you see where the problem lies? Thank you, Eva On 9/18/12 8:58 AM, reising...@rostlab.informatik.tu-muenchen.de wrote: Okey, now I tried it without any fixed residues. But still the energy after the minimization is not very low and I still get the LINCS warnings. The mdp file I use for the minimization looks like this: define = -DPOSRES Restraints during minimization generally restrict motion in the same way that freezing does. Again, this is a potential barrier to sufficient minimization. integrator = steep emtol = 10 nsteps = 1500 nstenergy = 1 energygrps
Re: [gmx-users] LINCS warning in md run
On 9/20/12 6:52 AM, reising...@rostlab.informatik.tu-muenchen.de wrote: Hi, now I tried it without any restriction and still the LINCS warnings occur. Since it is always the hydrogen atom where the huge force lies on I had the idea just to remove the hydrogen atom to find out whether another atom will occur to have such a high force on or everything went fine. And indeed, without the hydrogen atom there is no problem during the MD run. Even when I fix all the other atoms. I can not see why this occurs. I already looked at the residue with pymol and I could see that there is no other residue or atom clashing with it. I suspect what is happening is that the topology is not stable. If removal of the H atom leads to stable trajectories, then it is experiencing some interaction that leads to the crash. Likely what is happening is that it is experiencing a very strong 1-4 interaction with the other phosphate oxygens and is being pulled very hard away from the oxygen to which it is bonded, leading to deformed geometry and the LINCS warnings. There are two possible solutions: 1. Modify the 1-4 interactions through an appropriate pair term. 2. Add exclusions to the topology between the H atom and each of the O atoms to which it is not bonded. I would recommend testing with a very simple system of TYP in water to validate that the topology is stable and rule out other factors. -Justin The residue looks like this: ATOM955 N TYP65 27.310 23.150 27.670 1.00 0.00 N ATOM956 CA TYP65 26.870 23.320 26.300 1.00 0.00 C ATOM957 C TYP65 27.920 23.760 25.300 1.00 0.00 C ATOM958 O TYP65 28.060 23.210 24.210 1.00 0.00 O ATOM959 CB TYP65 25.740 24.340 26.170 1.00 0.00 C ATOM960 CG TYP65 24.530 23.740 26.830 1.00 0.00 C ATOM961 CD1 TYP65 24.410 23.760 28.220 1.00 0.00 C ATOM962 CD2 TYP65 23.510 23.180 26.050 1.00 0.00 C ATOM963 CE1 TYP65 23.290 23.210 28.840 1.00 0.00 C ATOM964 CE2 TYP65 22.380 22.630 26.660 1.00 0.00 C ATOM965 CZ TYP65 22.260 22.630 28.070 1.00 0.00 C ATOM966 OH TYP65 21.160 22.100 28.670 1.00 0.00 O ATOM967 P TYP65 20.298 21.422 27.722 1.00 0.00 P ATOM968 OP1 TYP65 21.003 21.245 26.467 1.00 0.00 O ATOM969 OP2 TYP65 19.920 20.126 28.251 1.00 0.00 O ATOM970 OP3 TYP65 19.106 22.218 27.498 1.00 0.00 O ATOM971 H TYP65 27.210 23.914 28.325 1.00 0.00 H ATOM972 HA TYP65 26.485 22.366 25.933 1.00 0.00 H ATOM973 HB1 TYP65 25.524 24.543 25.119 1.00 0.00 H ATOM974 HB2 TYP65 26.010 25.270 26.669 1.00 0.00 H ATOM975 HD1 TYP65 25.154 24.234 28.821 1.00 0.00 H ATOM976 HD2 TYP65 23.603 23.156 24.973 1.00 0.00 H ATOM977 HE1 TYP65 23.200 23.222 29.916 1.00 0.00 H ATOM978 HE2 TYP65 21.603 22.189 26.053 1.00 0.00 H ATOM979 H1P TYP65 20.357 20.996 25.802 1.00 0.00 H The topology entry in the aminoacid.rtp file looks like this: [ TYP ] [ atoms ] NN -0.5163001 CACT 0.2755032 HAH1 0.0082233 CBCT -0.3540524 HB1HC 0.1103265 HB2HC 0.1103266 CGCA 0.1197287 CD1CA -0.1989388 HD1HA 0.1371439 CE1CA -0.284884 10 HE1HA 0.177179 11 CZC0.452616 12 OHOS -0.534452 13 HH0.293600 14 CE2CA -0.284884 15 HE2HA 0.177179 16 CD2CA -0.198938 17 HD2HA 0.137143 18 CC0.536600 19 OO -0.581900 20 PP1.393213 21 OP1OH -0.752821 22 OP2O2 -0.822464 23 OP3O2 -0.822464 24 H1PHO 0.423316 25 [ bonds ] N H NCA CAHA CACB CA C CB HB1 CB HB2 CBCG CG CD1 CG CD2 CD1 HD1 CD1 CE1 CE1 HE1 CE1CZ CZOS CZ CE2 OS P CE2 HE2 CE2 CD2 CD2 HD2 C O -C N P OP1 P OP2 P OP3 H1P OP1 [ impropers ] -CCA N H CA+N C O CG CE2 CD2 HD2 CZ CD2 CE2 HE2 CD1CZ CE1 HE1 CG CE1 CD1 HD1 CD1 CD2CGCB CE1 CE2CZOH The LINCS problems lie between the oxygen atom of the phosphate where a hydrogen atom is bound to (OP1)
Re: [gmx-users] LINCS warning in md run
Hi Justin, thank you a lot for your answer. I will try it. Best, Eva On 9/20/12 6:52 AM, reising...@rostlab.informatik.tu-muenchen.de wrote: Hi, now I tried it without any restriction and still the LINCS warnings occur. Since it is always the hydrogen atom where the huge force lies on I had the idea just to remove the hydrogen atom to find out whether another atom will occur to have such a high force on or everything went fine. And indeed, without the hydrogen atom there is no problem during the MD run. Even when I fix all the other atoms. I can not see why this occurs. I already looked at the residue with pymol and I could see that there is no other residue or atom clashing with it. I suspect what is happening is that the topology is not stable. If removal of the H atom leads to stable trajectories, then it is experiencing some interaction that leads to the crash. Likely what is happening is that it is experiencing a very strong 1-4 interaction with the other phosphate oxygens and is being pulled very hard away from the oxygen to which it is bonded, leading to deformed geometry and the LINCS warnings. There are two possible solutions: 1. Modify the 1-4 interactions through an appropriate pair term. 2. Add exclusions to the topology between the H atom and each of the O atoms to which it is not bonded. I would recommend testing with a very simple system of TYP in water to validate that the topology is stable and rule out other factors. -Justin The residue looks like this: ATOM955 N TYP65 27.310 23.150 27.670 1.00 0.00 N ATOM956 CA TYP65 26.870 23.320 26.300 1.00 0.00 C ATOM957 C TYP65 27.920 23.760 25.300 1.00 0.00 C ATOM958 O TYP65 28.060 23.210 24.210 1.00 0.00 O ATOM959 CB TYP65 25.740 24.340 26.170 1.00 0.00 C ATOM960 CG TYP65 24.530 23.740 26.830 1.00 0.00 C ATOM961 CD1 TYP65 24.410 23.760 28.220 1.00 0.00 C ATOM962 CD2 TYP65 23.510 23.180 26.050 1.00 0.00 C ATOM963 CE1 TYP65 23.290 23.210 28.840 1.00 0.00 C ATOM964 CE2 TYP65 22.380 22.630 26.660 1.00 0.00 C ATOM965 CZ TYP65 22.260 22.630 28.070 1.00 0.00 C ATOM966 OH TYP65 21.160 22.100 28.670 1.00 0.00 O ATOM967 P TYP65 20.298 21.422 27.722 1.00 0.00 P ATOM968 OP1 TYP65 21.003 21.245 26.467 1.00 0.00 O ATOM969 OP2 TYP65 19.920 20.126 28.251 1.00 0.00 O ATOM970 OP3 TYP65 19.106 22.218 27.498 1.00 0.00 O ATOM971 H TYP65 27.210 23.914 28.325 1.00 0.00 H ATOM972 HA TYP65 26.485 22.366 25.933 1.00 0.00 H ATOM973 HB1 TYP65 25.524 24.543 25.119 1.00 0.00 H ATOM974 HB2 TYP65 26.010 25.270 26.669 1.00 0.00 H ATOM975 HD1 TYP65 25.154 24.234 28.821 1.00 0.00 H ATOM976 HD2 TYP65 23.603 23.156 24.973 1.00 0.00 H ATOM977 HE1 TYP65 23.200 23.222 29.916 1.00 0.00 H ATOM978 HE2 TYP65 21.603 22.189 26.053 1.00 0.00 H ATOM979 H1P TYP65 20.357 20.996 25.802 1.00 0.00 H The topology entry in the aminoacid.rtp file looks like this: [ TYP ] [ atoms ] NN -0.5163001 CACT 0.2755032 HAH1 0.0082233 CBCT -0.3540524 HB1HC 0.1103265 HB2HC 0.1103266 CGCA 0.1197287 CD1CA -0.1989388 HD1HA 0.1371439 CE1CA -0.284884 10 HE1HA 0.177179 11 CZC0.452616 12 OHOS -0.534452 13 HH0.293600 14 CE2CA -0.284884 15 HE2HA 0.177179 16 CD2CA -0.198938 17 HD2HA 0.137143 18 CC0.536600 19 OO -0.581900 20 PP1.393213 21 OP1OH -0.752821 22 OP2O2 -0.822464 23 OP3O2 -0.822464 24 H1PHO 0.423316 25 [ bonds ] N H NCA CAHA CACB CA C CB HB1 CB HB2 CBCG CG CD1 CG CD2 CD1 HD1 CD1 CE1 CE1 HE1 CE1CZ CZOS CZ CE2 OS P CE2 HE2 CE2 CD2 CD2 HD2 C O -C N P OP1 P OP2 P OP3 H1P OP1 [ impropers ] -CCA N H CA+N C O CG CE2 CD2 HD2 CZ CD2 CE2 HE2 CD1
Re: [gmx-users] LINCS warning in md run
I need the rest of the structure just as it is now because I want to do electrostatic analysis with it. I just added the phosphate manually and so I want to minimize and run a short MD with it. I added the dihedraltype of the amber database (http://personalpages.manchester.ac.uk/staff/Richard.Bryce/amber/pro/frcmod_y1p) to the ffbonded file. And additionally I looked at the protein and made all the residues which could somehow influence the protein flexible so that eventual clashes can be repaired. But still I got the error: ..Step 3612, time 3.612 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.08, max 0.31 (between atoms 975 and 978) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 976979 32.60.0961 0.0960 0.0960 Step 3613, time 3.613 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.000237, max 0.001400 (between atoms 976 and 979) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 976979 33.40.0960 0.0959 0.0960 .. Too many LINCS warnings (1000) I already minimized the protein and everything was fine. There were no errors: Steepest Descents converged to machine precision in 15 steps, but did not reach the requested Fmax 10. Potential Energy = -7.7436938e+05 Maximum force = 8.6871973e+03 on atom 979 Norm of force = 7.1224258e+01 gcq#49: You Could Make More Money As a Butcher (F. Zappa) Steepest Descents converged to machine precision in 15 steps, but did not reach the requested Fmax 10. Potential Energy = -7.7436938e+05 Maximum force = 8.6871973e+03 on atom 979 Norm of force = 7.1224258e+01 And also during the grompp run there are no errors. Can you please help me to find out where the problem lies? Thank you, Eva On 9/13/12 5:50 AM, reising...@rostlab.informatik.tu-muenchen.de wrote: Ah okey. Thank you. I will write them. Hmm, but the protein is a crystal structure from pdb with a resolution of 1.2. I already added the hydrogen atoms to this structure and there I already minimized them and made a md run. And there were no errors. And now I only added the phosphate to the minimized structure. So I thought that I only had to minimize the phosphate and the residue it bound on. Or is there a mistake in my thought here? If adding the phosphate resulted in a crash, then clearly that's the problem. I don't understand why you would run EM on just the phosphate and keep the rest of the protein structure frozen. Again, that potentially prevents clashes from being resolved. I don't understand what value there is in only minimizing the phosphate. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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 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 warning in md run
On 9/18/12 7:22 AM, reising...@rostlab.informatik.tu-muenchen.de wrote: I need the rest of the structure just as it is now because I want to do electrostatic analysis with it. I just added the phosphate manually and so I want to minimize and run a short MD with it. I added the dihedraltype of the amber database (http://personalpages.manchester.ac.uk/staff/Richard.Bryce/amber/pro/frcmod_y1p) to the ffbonded file. And additionally I looked at the protein and made all the residues which could somehow influence the protein flexible so that eventual clashes can be repaired. But still I got the error: ..Step 3612, time 3.612 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.08, max 0.31 (between atoms 975 and 978) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 976979 32.60.0961 0.0960 0.0960 Step 3613, time 3.613 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.000237, max 0.001400 (between atoms 976 and 979) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 976979 33.40.0960 0.0959 0.0960 .. So what are these atoms? This gives you a hint at the origin of the problem. Have you followed the troubleshooting advice at http://www.gromacs.org/Documentation/Terminology/Blowing_Up#Diagnosing_an_Unstable_System? It covers basically everything anyone would suggest to you for these types of errors. Posting an .mdp file would be useful in case you're doing something wrong with respect to the run parameters. Too many LINCS warnings (1000) I already minimized the protein and everything was fine. There were no errors: These are results are not fine at all. The maximum force on atom 979 is huge, and that's what's causing things to spin out of control very early in the MD. -Justin Steepest Descents converged to machine precision in 15 steps, but did not reach the requested Fmax 10. Potential Energy = -7.7436938e+05 Maximum force = 8.6871973e+03 on atom 979 Norm of force = 7.1224258e+01 gcq#49: You Could Make More Money As a Butcher (F. Zappa) Steepest Descents converged to machine precision in 15 steps, but did not reach the requested Fmax 10. Potential Energy = -7.7436938e+05 Maximum force = 8.6871973e+03 on atom 979 Norm of force = 7.1224258e+01 And also during the grompp run there are no errors. Can you please help me to find out where the problem lies? Thank you, Eva On 9/13/12 5:50 AM, reising...@rostlab.informatik.tu-muenchen.de wrote: Ah okey. Thank you. I will write them. Hmm, but the protein is a crystal structure from pdb with a resolution of 1.2. I already added the hydrogen atoms to this structure and there I already minimized them and made a md run. And there were no errors. And now I only added the phosphate to the minimized structure. So I thought that I only had to minimize the phosphate and the residue it bound on. Or is there a mistake in my thought here? If adding the phosphate resulted in a crash, then clearly that's the problem. I don't understand why you would run EM on just the phosphate and keep the rest of the protein structure frozen. Again, that potentially prevents clashes from being resolved. I don't understand what value there is in only minimizing the phosphate. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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 -- Justin A. Lemkul, Ph.D. Research Scientist 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
Re: [gmx-users] LINCS warning in md run
Looks like there is still something clashing with atom 979. The resulting force after EM was close to 1, which is not very much minimized at all... What is atom 979 and what is near it? On 2012-09-18 01:22:25PM +0200, reising...@rostlab.informatik.tu-muenchen.de wrote: I need the rest of the structure just as it is now because I want to do electrostatic analysis with it. I just added the phosphate manually and so I want to minimize and run a short MD with it. I added the dihedraltype of the amber database (http://personalpages.manchester.ac.uk/staff/Richard.Bryce/amber/pro/frcmod_y1p) to the ffbonded file. And additionally I looked at the protein and made all the residues which could somehow influence the protein flexible so that eventual clashes can be repaired. But still I got the error: ..Step 3612, time 3.612 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.08, max 0.31 (between atoms 975 and 978) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 976979 32.60.0961 0.0960 0.0960 Step 3613, time 3.613 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.000237, max 0.001400 (between atoms 976 and 979) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 976979 33.40.0960 0.0959 0.0960 .. Too many LINCS warnings (1000) I already minimized the protein and everything was fine. There were no errors: Steepest Descents converged to machine precision in 15 steps, but did not reach the requested Fmax 10. Potential Energy = -7.7436938e+05 Maximum force = 8.6871973e+03 on atom 979 Norm of force = 7.1224258e+01 gcq#49: You Could Make More Money As a Butcher (F. Zappa) Steepest Descents converged to machine precision in 15 steps, but did not reach the requested Fmax 10. Potential Energy = -7.7436938e+05 Maximum force = 8.6871973e+03 on atom 979 Norm of force = 7.1224258e+01 And also during the grompp run there are no errors. Can you please help me to find out where the problem lies? Thank you, Eva On 9/13/12 5:50 AM, reising...@rostlab.informatik.tu-muenchen.de wrote: Ah okey. Thank you. I will write them. Hmm, but the protein is a crystal structure from pdb with a resolution of 1.2. I already added the hydrogen atoms to this structure and there I already minimized them and made a md run. And there were no errors. And now I only added the phosphate to the minimized structure. So I thought that I only had to minimize the phosphate and the residue it bound on. Or is there a mistake in my thought here? If adding the phosphate resulted in a crash, then clearly that's the problem. I don't understand why you would run EM on just the phosphate and keep the rest of the protein structure frozen. Again, that potentially prevents clashes from being resolved. I don't understand what value there is in only minimizing the phosphate. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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 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 -- == Peter C. Lai| University of Alabama-Birmingham Programmer/Analyst | KAUL 752A Genetics, Div. of Research | 705 South 20th Street p...@uab.edu| Birmingham AL 35294-4461 (205) 690-0808 | == -- 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
Re: [gmx-users] LINCS warning in md run
On 9/18/12 7:22 AM, reising...@rostlab.informatik.tu-muenchen.de wrote: I need the rest of the structure just as it is now because I want to do electrostatic analysis with it. Another thing worth considering - why do you necessarily need the rest of the structure to be identical? Or perhaps better stated, why do you believe this to be the more appropriate model of reality? Phosphorylation events frequently trigger structural changes in the protein, so I see no reason to assume it will have no effect on the rest of the structure. At the very least, you can try a normal EM and MD procedure without freezing anything to see if you can determine the problem. If things run normally without freezing, then you know that whatever you are doing here is artificial and problematic. -Justin I just added the phosphate manually and so I want to minimize and run a short MD with it. I added the dihedraltype of the amber database (http://personalpages.manchester.ac.uk/staff/Richard.Bryce/amber/pro/frcmod_y1p) to the ffbonded file. And additionally I looked at the protein and made all the residues which could somehow influence the protein flexible so that eventual clashes can be repaired. But still I got the error: ..Step 3612, time 3.612 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.08, max 0.31 (between atoms 975 and 978) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 976979 32.60.0961 0.0960 0.0960 Step 3613, time 3.613 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.000237, max 0.001400 (between atoms 976 and 979) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 976979 33.40.0960 0.0959 0.0960 .. Too many LINCS warnings (1000) I already minimized the protein and everything was fine. There were no errors: Steepest Descents converged to machine precision in 15 steps, but did not reach the requested Fmax 10. Potential Energy = -7.7436938e+05 Maximum force = 8.6871973e+03 on atom 979 Norm of force = 7.1224258e+01 gcq#49: You Could Make More Money As a Butcher (F. Zappa) Steepest Descents converged to machine precision in 15 steps, but did not reach the requested Fmax 10. Potential Energy = -7.7436938e+05 Maximum force = 8.6871973e+03 on atom 979 Norm of force = 7.1224258e+01 And also during the grompp run there are no errors. Can you please help me to find out where the problem lies? Thank you, Eva On 9/13/12 5:50 AM, reising...@rostlab.informatik.tu-muenchen.de wrote: Ah okey. Thank you. I will write them. Hmm, but the protein is a crystal structure from pdb with a resolution of 1.2. I already added the hydrogen atoms to this structure and there I already minimized them and made a md run. And there were no errors. And now I only added the phosphate to the minimized structure. So I thought that I only had to minimize the phosphate and the residue it bound on. Or is there a mistake in my thought here? If adding the phosphate resulted in a crash, then clearly that's the problem. I don't understand why you would run EM on just the phosphate and keep the rest of the protein structure frozen. Again, that potentially prevents clashes from being resolved. I don't understand what value there is in only minimizing the phosphate. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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 -- Justin A. Lemkul, Ph.D. Research Scientist 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
Re: [gmx-users] LINCS warning in md run
Okey, now I tried it without any fixed residues. But still the energy after the minimization is not very low and I still get the LINCS warnings. The mdp file I use for the minimization looks like this: define = -DPOSRES integrator = steep emtol = 10 nsteps = 1500 nstenergy = 1 energygrps = System coulombtype = PME rcoulomb= 0.9 rvdw= 0.9 rlist = 0.9 fourierspacing = 0.12 pme_order = 4 ewald_rtol = 1e-5 pbc = xyz the mdp file for the md run looks like this: define = -DPOSRES integrator = md dt = 0.001 nsteps = 5000 nstxout = 100 nstvout = 0 nstfout = 0 nstlog = 1000 nstxtcout = 500 nstenergy = 5 energygrps = Protein Non-Protein nstcalcenergy = 5 nstlist = 10 ns-type = Grid pbc = xyz rlist = 0.9 coulombtype = PME rcoulomb= 0.9 rvdw= 0.9 fourierspacing = 0.12 pme_order = 4 ewald_rtol = 1e-5 gen_vel = yes gen_temp= 200.0 gen_seed= constraints = all-bonds tcoupl = V-rescale tc-grps = Protein Non-Protein tau_t = 0.1 0.1 ref_t = 298 298 pcoupl = no The output of the minimization run is: Steepest Descents converged to machine precision in 15 steps, but did not reach the requested Fmax 10. Potential Energy = -7.9280412e+05 Maximum force = 1.0772942e+04 on atom 979 Norm of force = 9.6685356e+01 The output of the MD run is: Step 1031, time 1.031 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.001431, max 0.010707 (between atoms 976 and 979) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 976979 81.60.1272 0.0970 0.0960 The atom 979 is the hydrogen atom on the phosphate. There has to be one hydrogen atoms because it is protonated once. The other atom 976 is the oxygen atom where the hydrogen atom is bound to. The bounding parameters for this kind of binding were already there. I didn't add them. I already did it for another phosphorylation on another position in this structure. And here I also got many LINCS errors. And again the problem is the connection between the hydrogen atom and the oxygen atom. But I do not understand why. Can you please help me?! On 9/18/12 7:22 AM, reising...@rostlab.informatik.tu-muenchen.de wrote: I need the rest of the structure just as it is now because I want to do electrostatic analysis with it. Another thing worth considering - why do you necessarily need the rest of the structure to be identical? Or perhaps better stated, why do you believe this to be the more appropriate model of reality? Phosphorylation events frequently trigger structural changes in the protein, so I see no reason to assume it will have no effect on the rest of the structure. At the very least, you can try a normal EM and MD procedure without freezing anything to see if you can determine the problem. If things run normally without freezing, then you know that whatever you are doing here is artificial and problematic. -Justin I just added the phosphate manually and so I want to minimize and run a short MD with it. I added the dihedraltype of the amber database (http://personalpages.manchester.ac.uk/staff/Richard.Bryce/amber/pro/frcmod_y1p) to the ffbonded file. And additionally I looked at the protein and made all the residues which could somehow influence the protein flexible so that eventual clashes can be repaired. But still I got the error: ..Step 3612, time 3.612 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.08, max 0.31 (between atoms 975 and 978) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 976979 32.60.0961 0.0960 0.0960 Step 3613, time 3.613 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.000237, max 0.001400 (between atoms 976 and 979) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 976979 33.40.0960 0.0959 0.0960 .. Too many LINCS warnings (1000) I already minimized the protein and everything was fine. There were no errors: Steepest Descents converged to machine precision in 15 steps, but did not reach the requested Fmax 10. Potential Energy = -7.7436938e+05 Maximum force = 8.6871973e+03 on atom 979 Norm of force = 7.1224258e+01 gcq#49: You Could Make More Money As a Butcher (F. Zappa) Steepest Descents converged to machine
Re: [gmx-users] LINCS warning in md run
On 9/18/12 8:58 AM, reising...@rostlab.informatik.tu-muenchen.de wrote: Okey, now I tried it without any fixed residues. But still the energy after the minimization is not very low and I still get the LINCS warnings. The mdp file I use for the minimization looks like this: define = -DPOSRES Restraints during minimization generally restrict motion in the same way that freezing does. Again, this is a potential barrier to sufficient minimization. integrator = steep emtol = 10 nsteps = 1500 nstenergy = 1 energygrps = System coulombtype = PME rcoulomb= 0.9 rvdw= 0.9 rlist = 0.9 fourierspacing = 0.12 pme_order = 4 ewald_rtol = 1e-5 pbc = xyz the mdp file for the md run looks like this: define = -DPOSRES integrator = md dt = 0.001 nsteps = 5000 nstxout = 100 nstvout = 0 nstfout = 0 nstlog = 1000 nstxtcout = 500 nstenergy = 5 energygrps = Protein Non-Protein nstcalcenergy = 5 nstlist = 10 ns-type = Grid pbc = xyz rlist = 0.9 coulombtype = PME rcoulomb= 0.9 rvdw= 0.9 fourierspacing = 0.12 pme_order = 4 ewald_rtol = 1e-5 gen_vel = yes gen_temp= 200.0 gen_seed= constraints = all-bonds tcoupl = V-rescale tc-grps = Protein Non-Protein tau_t = 0.1 0.1 ref_t = 298 298 pcoupl = no The output of the minimization run is: Steepest Descents converged to machine precision in 15 steps, but did not reach the requested Fmax 10. Potential Energy = -7.9280412e+05 Maximum force = 1.0772942e+04 on atom 979 Norm of force = 9.6685356e+01 Note that this outcome is even worse than before. The maximum force is now over 10,000. The output of the MD run is: Step 1031, time 1.031 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.001431, max 0.010707 (between atoms 976 and 979) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 976979 81.60.1272 0.0970 0.0960 As you should expect. If you can't get a reasonable minimization, the MD will always crash. The atom 979 is the hydrogen atom on the phosphate. There has to be one hydrogen atoms because it is protonated once. The other atom 976 is the oxygen atom where the hydrogen atom is bound to. The bounding parameters for this kind of binding were already there. I didn't add them. I already did it for another phosphorylation on another position in this structure. And here I also got many LINCS errors. And again the problem is the connection between the hydrogen atom and the oxygen atom. But I do not understand why. Remove all restraints/freezing/whatever in the .mdp file and try the EM again. If it still does not converge to a reasonable value, then there are two potential problems: 1. The topology is flawed and thus the structure cannot be run stably 2. The structure cannot accommodate phosphate in this location and due to unresolvable clashes, the runs fail -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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
Re: [gmx-users] LINCS warning in md run
On 9/13/12 4:22 AM, reising...@rostlab.informatik.tu-muenchen.de wrote: Hi Justin, this atom is the CG atom of the phosphate I added to the protein. But how can I find out by what it is punished? Visualization. This is the topology for this residue in the aminoacid.rtp file. I added it manually. The parameter are from the amber parameter database (http://www.pharmacy.manchester.ac.uk/bryce/amber/): [ TYP ] [ atoms ] NN -0.5163001 CACT 0.2755032 HAH1 0.0082233 CBCT -0.3540524 HB1HC 0.1103265 HB2HC 0.1103266 CGCA 0.1197287 CD1CA -0.1989388 HD1HA 0.1371439 CE1CA -0.284884 10 HE1HA 0.177179 11 CZC0.452616 12 OHOS -0.534452 13 HH0.293600 14 CE2CA -0.284884 15 HE2HA 0.177179 16 CD2CA -0.198938 17 HD2HA 0.137143 18 CC0.536600 19 OO -0.581900 20 PP1.393213 21 OP1OH -0.752821 22 OP2O2 -0.822464 23 OP3O2 -0.822464 24 H1PHO 0.423316 25 [ bonds ] N H NCA CAHA CACB CA C CB HB1 CB HB2 CBCG CG CD1 CG CD2 CD1 HD1 CD1 CE1 CE1 HE1 CE1CZ CZOS CZ CE2 OS P CE2 HE2 CE2 CD2 CD2 HD2 C O -C N P OP1 P OP2 P OP3 OP1 H1P [ impropers ] -CCA N H CA+N C O CG CE2 CD2 HD2 CZ CD2 CE2 HE2 CD1CZ CE1 HE1 CG CE1 CD1 HD1 CD1 CD2CGCB CE1 CE2CZOH Additionally I had to add an entry in the ffbonded file in the part [ dihedraltypes ] CA CA C OS 4 180.00 4.60240 2; Here I am not completely sure about the entry because I could not find a source for this combination of atoms. But there is already an entry for the combination CA CA C OH Which has the same parameters. Could this be the problem? And if it could be, can you please give me hint where I can find parameters for it? Because I really could not find it. Potentially - if you haphazardly assign parameters, you may get unexpected results. There is a cited reference for the TYP parameters at the website above. I would suggest looking there first, and if there is nothing listed, then contact the corresponding author of the study that first used/derived the parameters. Additionally, if you freeze a part of the protein's structure, you prevent any existing clashes from being resolved. That may be the root of the issue. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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
Re: [gmx-users] LINCS warning in md run
Ah okey. Thank you. I will write them. Hmm, but the protein is a crystal structure from pdb with a resolution of 1.2. I already added the hydrogen atoms to this structure and there I already minimized them and made a md run. And there were no errors. And now I only added the phosphate to the minimized structure. So I thought that I only had to minimize the phosphate and the residue it bound on. Or is there a mistake in my thought here? On 9/13/12 4:22 AM, reising...@rostlab.informatik.tu-muenchen.de wrote: Hi Justin, this atom is the CG atom of the phosphate I added to the protein. But how can I find out by what it is punished? Visualization. This is the topology for this residue in the aminoacid.rtp file. I added it manually. The parameter are from the amber parameter database (http://www.pharmacy.manchester.ac.uk/bryce/amber/): [ TYP ] [ atoms ] NN -0.5163001 CACT 0.2755032 HAH1 0.0082233 CBCT -0.3540524 HB1HC 0.1103265 HB2HC 0.1103266 CGCA 0.1197287 CD1CA -0.1989388 HD1HA 0.1371439 CE1CA -0.284884 10 HE1HA 0.177179 11 CZC0.452616 12 OHOS -0.534452 13 HH0.293600 14 CE2CA -0.284884 15 HE2HA 0.177179 16 CD2CA -0.198938 17 HD2HA 0.137143 18 CC0.536600 19 OO -0.581900 20 PP1.393213 21 OP1OH -0.752821 22 OP2O2 -0.822464 23 OP3O2 -0.822464 24 H1PHO 0.423316 25 [ bonds ] N H NCA CAHA CACB CA C CB HB1 CB HB2 CBCG CG CD1 CG CD2 CD1 HD1 CD1 CE1 CE1 HE1 CE1CZ CZOS CZ CE2 OS P CE2 HE2 CE2 CD2 CD2 HD2 C O -C N P OP1 P OP2 P OP3 OP1 H1P [ impropers ] -CCA N H CA+N C O CG CE2 CD2 HD2 CZ CD2 CE2 HE2 CD1CZ CE1 HE1 CG CE1 CD1 HD1 CD1 CD2CGCB CE1 CE2CZOH Additionally I had to add an entry in the ffbonded file in the part [ dihedraltypes ] CA CA C OS 4 180.00 4.60240 2; Here I am not completely sure about the entry because I could not find a source for this combination of atoms. But there is already an entry for the combination CA CA C OH Which has the same parameters. Could this be the problem? And if it could be, can you please give me hint where I can find parameters for it? Because I really could not find it. Potentially - if you haphazardly assign parameters, you may get unexpected results. There is a cited reference for the TYP parameters at the website above. I would suggest looking there first, and if there is nothing listed, then contact the corresponding author of the study that first used/derived the parameters. Additionally, if you freeze a part of the protein's structure, you prevent any existing clashes from being resolved. That may be the root of the issue. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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 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 warning in md run
On 9/13/12 5:50 AM, reising...@rostlab.informatik.tu-muenchen.de wrote: Ah okey. Thank you. I will write them. Hmm, but the protein is a crystal structure from pdb with a resolution of 1.2. I already added the hydrogen atoms to this structure and there I already minimized them and made a md run. And there were no errors. And now I only added the phosphate to the minimized structure. So I thought that I only had to minimize the phosphate and the residue it bound on. Or is there a mistake in my thought here? If adding the phosphate resulted in a crash, then clearly that's the problem. I don't understand why you would run EM on just the phosphate and keep the rest of the protein structure frozen. Again, that potentially prevents clashes from being resolved. I don't understand what value there is in only minimizing the phosphate. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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
Re: [gmx-users] LINCS warning in md run
On 9/12/12 6:57 AM, reising...@rostlab.informatik.tu-muenchen.de wrote: Hi everybody, during the mdrun_mpi I get many LINCS warnings like for example: Step 1143, time 1.143 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.265373, max 1.416702 (between atoms 976 and 979) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 976979 90.00.1072 0.2320 0.0960 But I don't know why. I already minimized my protein. And also in the grompp run there were no error messages. This was the end of my grompp output: processing index file... Making dummy/rest group for Acceleration containing 80212 elements Making dummy/rest group for Freeze containing 51274 elements Making dummy/rest group for VCM containing 80212 elements Number of degrees of freedom in T-Coupling group System is 102623.00 Making dummy/rest group for User1 containing 80212 elements Making dummy/rest group for User2 containing 80212 elements Making dummy/rest group for XTC containing 80212 elements Making dummy/rest group for Or. Res. Fit containing 80212 elements Making dummy/rest group for QMMM containing 80212 elements T-Coupling has 1 element(s): System Energy Mon. has 2 element(s): Protein non-Protein Acceleration has 1 element(s): rest Freeze has 2 element(s): Protein__!TYP rest User1has 1 element(s): rest User2has 1 element(s): rest VCM has 1 element(s): rest XTC has 1 element(s): rest Or. Res. Fit has 1 element(s): rest QMMM has 1 element(s): rest Checking consistency between energy and charge groups... Estimate for the relative computational load of the PME mesh part: 0.32 writing run input file... Can you please help me? http://www.gromacs.org/Documentation/Terminology/Blowing_Up Without a complete description of your system (its contents, previous minimization and equilibration and their success/failure) and any relevant .mdp file(s), there's little else that anyone can say. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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
Re: [gmx-users] LINCS warning in md run
Hi Justin, my mdp file for the md run looks like this: define = -DPOSRES integrator = md dt = 0.001 nsteps = 5000 nstxout = 100 nstvout = 0 nstfout = 0 nstlog = 1000 nstxtcout = 500 nstenergy = 5 energygrps = Protein Non-Protein nstcalcenergy = 5 nstlist = 10 ns-type = Grid pbc = xyz rlist = 0.9 coulombtype = PME rcoulomb= 0.9 rvdw= 0.9 fourierspacing = 0.12 pme_order = 4 ewald_rtol = 1e-5 gen_vel = yes gen_temp= 200.0 gen_seed= constraints = all-bonds tcoupl = V-rescale tc-grps = Protein System__!Protein tau_t = 0.1 0.1 ref_t = 298 298 pcoupl = no freezegrps = Protein__!TYP freezedim = Y Y Y I added a phosphate (TYP) to my protein and now want to do first a minimization (which I already did), then a short md run (for the case that I am in a local minima) and after that again a minimization. Since I only want to minimize the energy of the phosphate I freezed the rest of the protein (Protein__!TYP). Since on my cluster I am not allowed to run long jobs I had to divide the minimization run in several runs. The output of the last run was: Steepest Descents converged to machine precision in 15 steps, but did not reach the requested Fmax 10. Potential Energy = -7.7264606e+05 Maximum force = 1.6227990e+04 on atom 961 Norm of force = 1.2328220e+02 gcq#192: It's So Fast It's Slow (F. Black) Steepest Descents converged to machine precision in 15 steps, but did not reach the requested Fmax 10. Potential Energy = -7.7264606e+05 Maximum force = 1.6227990e+04 on atom 961 Norm of force = 1.2328220e+02 After this minimization run I wanted to do the md run. My protein is a membrane protein with its surrounding membrane. I already did a minimization and md run with this protein but without the phosphate. The only difference to the time when everything worked fine is the phosphate. Does this help you somehow to see the failure? Thank you!! On 9/12/12 6:57 AM, reising...@rostlab.informatik.tu-muenchen.de wrote: Hi everybody, during the mdrun_mpi I get many LINCS warnings like for example: Step 1143, time 1.143 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.265373, max 1.416702 (between atoms 976 and 979) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 976979 90.00.1072 0.2320 0.0960 But I don't know why. I already minimized my protein. And also in the grompp run there were no error messages. This was the end of my grompp output: processing index file... Making dummy/rest group for Acceleration containing 80212 elements Making dummy/rest group for Freeze containing 51274 elements Making dummy/rest group for VCM containing 80212 elements Number of degrees of freedom in T-Coupling group System is 102623.00 Making dummy/rest group for User1 containing 80212 elements Making dummy/rest group for User2 containing 80212 elements Making dummy/rest group for XTC containing 80212 elements Making dummy/rest group for Or. Res. Fit containing 80212 elements Making dummy/rest group for QMMM containing 80212 elements T-Coupling has 1 element(s): System Energy Mon. has 2 element(s): Protein non-Protein Acceleration has 1 element(s): rest Freeze has 2 element(s): Protein__!TYP rest User1has 1 element(s): rest User2has 1 element(s): rest VCM has 1 element(s): rest XTC has 1 element(s): rest Or. Res. Fit has 1 element(s): rest QMMM has 1 element(s): rest Checking consistency between energy and charge groups... Estimate for the relative computational load of the PME mesh part: 0.32 writing run input file... Can you please help me? http://www.gromacs.org/Documentation/Terminology/Blowing_Up Without a complete description of your system (its contents, previous minimization and equilibration and their success/failure) and any relevant .mdp file(s), there's little else that anyone can say. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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
Re: [gmx-users] LINCS warning in md run
On 9/12/12 3:39 PM, reising...@rostlab.informatik.tu-muenchen.de wrote: Hi Justin, my mdp file for the md run looks like this: define = -DPOSRES integrator = md dt = 0.001 nsteps = 5000 nstxout = 100 nstvout = 0 nstfout = 0 nstlog = 1000 nstxtcout = 500 nstenergy = 5 energygrps = Protein Non-Protein nstcalcenergy = 5 nstlist = 10 ns-type = Grid pbc = xyz rlist = 0.9 coulombtype = PME rcoulomb= 0.9 rvdw= 0.9 fourierspacing = 0.12 pme_order = 4 ewald_rtol = 1e-5 gen_vel = yes gen_temp= 200.0 gen_seed= constraints = all-bonds tcoupl = V-rescale tc-grps = Protein System__!Protein tau_t = 0.1 0.1 ref_t = 298 298 pcoupl = no freezegrps = Protein__!TYP freezedim = Y Y Y I added a phosphate (TYP) to my protein and now want to do first a minimization (which I already did), then a short md run (for the case that I am in a local minima) and after that again a minimization. Since I only want to minimize the energy of the phosphate I freezed the rest of the protein (Protein__!TYP). Since on my cluster I am not allowed to run long jobs I had to divide the minimization run in several runs. The output of the last run was: Steepest Descents converged to machine precision in 15 steps, but did not reach the requested Fmax 10. Potential Energy = -7.7264606e+05 Maximum force = 1.6227990e+04 on atom 961 Norm of force = 1.2328220e+02 gcq#192: It's So Fast It's Slow (F. Black) Steepest Descents converged to machine precision in 15 steps, but did not reach the requested Fmax 10. Potential Energy = -7.7264606e+05 Maximum force = 1.6227990e+04 on atom 961 Norm of force = 1.2328220e+02 After this minimization run I wanted to do the md run. My protein is a membrane protein with its surrounding membrane. I already did a minimization and md run with this protein but without the phosphate. The only difference to the time when everything worked fine is the phosphate. Does this help you somehow to see the failure? Your minimization is insufficient. You have a maximum force in excess of 16000 on atom 961. Such a large force explains the crash. You should investigate what this atom is and what is pushing on it so hard. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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
Re: [gmx-users] LINCS warning and segmentation fault for methane in 1-octanol simulation
vivek sharma wrote: Hi There, I was trying to run a equilibrium run (npt) for system of Methane in 1-octanol (1 methane molecule with 200 1-octanol molecules with OPLS FF parameters). Following is the series of steps I followed: 1. Energy minimization with steep integrator for 5000 steps 2. Energy minimization with l-bfgs integrator for 5000 steps 3. NVT run for 100 ps with sd integrator 4. NPT run for 100 ps with sd integrator (with Pcoupl = Parrinello-Rahman, tau_p = 0.5, compressibility = 4.5e-05, ref_p = 1.0) During the NPT run I am ending up with following error (too many LINCS warning): - Step 25406, time 50.812 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 11.778495, max 363.475445 (between atoms 2158 and 2157) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 2152 2150 90.00.1090 1.3690 0.1090 2152 2151 90.00.1090 36.5266 0.1090 2158 2156 90.00.1091 0.5637 0.1090 2158 2157 90.00.2349 39.7278 0.1090 Back Off! I just backed up step25406b_n0.pdb to ./#step25406b_n0.pdb.1# Back Off! I just backed up step25406c_n0.pdb to ./#step25406c_n0.pdb.1# Wrote pdb files with previous and current coordinates Segmentation fault *.mdp files for above simulation are adapted from tutorial on free energy calculation by Justin. Please suggest me what could be wrong with above simulation. The answer for LINCS warnings is always the same - the system has become unstable due to inappropriate geometry, bad .mdp settings, or a combination of both. To troubleshoot, start by turning off the free energy code to make sure your system is actually stable. If it's not, refer here: http://www.gromacs.org/Documentation/Terminology/Blowing_Up#Diagnosing_an_Unstable_System If it is stable, turn back on whatever free energy settings you're using. I assume, based on the tutorial, that this is a simple vdW transformation? -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
Re: [gmx-users] LINCS warning and segmentation fault for methane in 1-octanol simulation
Hi Justin, Thanks for your response. After posting my query, I tried running the similar set with NPT run for 100 ps with sd integrator (with Pcoupl = berensen, tau_p = 0.5, compressibility = 4.5e-05, ref_p = 1.0) On giving berendsen instead of Parrinello-Rahman for pressure coupling, job finished successfully. Can you comment on this? As par the tutorial I am using simple vdW transformation only as mentioned below - couple-moltype = Methane ; name of moleculetype to decouple couple-lambda0 = vdw ; only van der Waals interactions couple-lambda1 = none ; turn off everything, in this case only vdW - Thanks, Vivek On 09/02/2012, Justin A. Lemkul jalem...@vt.edu wrote: vivek sharma wrote: Hi There, I was trying to run a equilibrium run (npt) for system of Methane in 1-octanol (1 methane molecule with 200 1-octanol molecules with OPLS FF parameters). Following is the series of steps I followed: 1. Energy minimization with steep integrator for 5000 steps 2. Energy minimization with l-bfgs integrator for 5000 steps 3. NVT run for 100 ps with sd integrator 4. NPT run for 100 ps with sd integrator (with Pcoupl = Parrinello-Rahman, tau_p = 0.5, compressibility = 4.5e-05, ref_p = 1.0) During the NPT run I am ending up with following error (too many LINCS warning): - Step 25406, time 50.812 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 11.778495, max 363.475445 (between atoms 2158 and 2157) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 2152 2150 90.00.1090 1.3690 0.1090 2152 2151 90.00.1090 36.5266 0.1090 2158 2156 90.00.1091 0.5637 0.1090 2158 2157 90.00.2349 39.7278 0.1090 Back Off! I just backed up step25406b_n0.pdb to ./#step25406b_n0.pdb.1# Back Off! I just backed up step25406c_n0.pdb to ./#step25406c_n0.pdb.1# Wrote pdb files with previous and current coordinates Segmentation fault *.mdp files for above simulation are adapted from tutorial on free energy calculation by Justin. Please suggest me what could be wrong with above simulation. The answer for LINCS warnings is always the same - the system has become unstable due to inappropriate geometry, bad .mdp settings, or a combination of both. To troubleshoot, start by turning off the free energy code to make sure your system is actually stable. If it's not, refer here: http://www.gromacs.org/Documentation/Terminology/Blowing_Up#Diagnosing_an_Unstable_System If it is stable, turn back on whatever free energy settings you're using. I assume, based on the tutorial, that this is a simple vdW transformation? -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 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 warning and segmentation fault for methane in 1-octanol simulation
On 10/02/2012 4:41 PM, vivek sharma wrote: Hi Justin, Thanks for your response. After posting my query, I tried running the similar set with NPT run for 100 ps with sd integrator (with Pcoupl = berensen, tau_p = 0.5, compressibility = 4.5e-05, ref_p = 1.0) On giving berendsen instead of Parrinello-Rahman for pressure coupling, job finished successfully. Can you comment on this? I suggest you read the manual section on pressure coupling, which likely explains this observation. Mark As par the tutorial I am using simple vdW transformation only as mentioned below - couple-moltype = Methane ; name of moleculetype to decouple couple-lambda0 = vdw ; only van der Waals interactions couple-lambda1 = none ; turn off everything, in this case only vdW - Thanks, Vivek On 09/02/2012, Justin A. Lemkuljalem...@vt.edu wrote: vivek sharma wrote: Hi There, I was trying to run a equilibrium run (npt) for system of Methane in 1-octanol (1 methane molecule with 200 1-octanol molecules with OPLS FF parameters). Following is the series of steps I followed: 1. Energy minimization with steep integrator for 5000 steps 2. Energy minimization with l-bfgs integrator for 5000 steps 3. NVT run for 100 ps with sd integrator 4. NPT run for 100 ps with sd integrator (with Pcoupl = Parrinello-Rahman, tau_p = 0.5, compressibility = 4.5e-05, ref_p = 1.0) During the NPT run I am ending up with following error (too many LINCS warning): - Step 25406, time 50.812 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 11.778495, max 363.475445 (between atoms 2158 and 2157) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 2152 2150 90.00.1090 1.3690 0.1090 2152 2151 90.00.1090 36.5266 0.1090 2158 2156 90.00.1091 0.5637 0.1090 2158 2157 90.00.2349 39.7278 0.1090 Back Off! I just backed up step25406b_n0.pdb to ./#step25406b_n0.pdb.1# Back Off! I just backed up step25406c_n0.pdb to ./#step25406c_n0.pdb.1# Wrote pdb files with previous and current coordinates Segmentation fault *.mdp files for above simulation are adapted from tutorial on free energy calculation by Justin. Please suggest me what could be wrong with above simulation. The answer for LINCS warnings is always the same - the system has become unstable due to inappropriate geometry, bad .mdp settings, or a combination of both. To troubleshoot, start by turning off the free energy code to make sure your system is actually stable. If it's not, refer here: http://www.gromacs.org/Documentation/Terminology/Blowing_Up#Diagnosing_an_Unstable_System If it is stable, turn back on whatever free energy settings you're using. I assume, based on the tutorial, that this is a simple vdW transformation? -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 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 warning on galactose molecule
On 23/03/2011 9:45 PM, Anna Marabotti wrote: Dear gmx-users, I'm experimenting a LINCS warning on my system, an enzyme with ATP, galactose and Mg. We started from the crystallographic structure, made some accommodation on the topology of the sugar in order to check for partial charges (according to Justin Lemkul's suggestions on PRODRG server), then performed a minimization, NVT and NPT PR-MD and the production MD. After about 5 ns of simulation the MD stopped with the LINCS error: Step 2562553, time 5125.11 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.000102, max 0.001903 (between atoms 7643 and 7642) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 7641 7640 45.3 0.1000 0.1000 0.1000 Step 2562554, time 5125.11 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.000104, max 0.001558 (between atoms 7643 and 7642) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 7641 7640 36.5 0.1000 0.1000 0.1000 Step 2562565, time 5125.13 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.000318, max 0.007712 (between atoms 7641 and 7640) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 7641 7640 31.5 0.1005 0.1008 0.1000 Step 2562566, time 5125.13 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.000374, max 0.009231 (between atoms 7641 and 7640) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 7641 7640 38.2 0.1008 0.1009 0.1000 Step 2562567, time 5125.13 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.000310, max 0.007658 (between atoms 7641 and 7640) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 7641 7640 38.6 0.1009 0.1008 0.1000 Step 2563563, time 5127.13 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.70, max 0.001640 (between atoms 7641 and 7640) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 7641 7640 57.0 0.0998 0.1002 0.1000 --- Program mdrun, VERSION 4.0.3 Source code file: constr.c, line: 136 Fatal error: Too many LINCS warnings (1000) 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 --- We checked the system to find the problem. The atoms 7641 and 7640 correspond to atom O1 and H12 of the galactose. With VMD we visualized the trajectory, but we did not see anything anomalous on this bond. Length and angles are quite normal. This OH group is near the phosphate of ATP but the distances seem to be compatible with an (expected) H-bond. I don't think the problem could be an incorrect stabilization because it seems to me that in that case the problem would have appear during the first step of MD, not after 5 ns. In any case, stabilization went correctly, with no errors or warnings. I checked on the gmx-users list and found some messages of Xavier Periole experimenting some LINCS problems with gmx 4.0.4, that seems to resemble my situation. I followed the thread, but I did not see anything that could be of help for me. Some hypotheses were about the gmx version (mine is 4.0.3), communications between CPUs, virtual sites. Looking at the trajectory, I don't think it's a problem of periodic images too close. The thread stops with Xavier saying he would like to test the effects of using -rdd and -rcon on LINCS warning, but I did not find the rest of the history. Does anybody (and especially Xavier, if possible!) have some hints about my problem? Or could it be a problem of galactose topology? Usually the problem has nothing to do with LINCS or -rdd or -con - they're just symptoms of machinery that breaks first. I'd start by assuming my topologies were not well-formed somehow, and divide and conquer to locate the problem. Can you simulate galactose in vacuo? In a small water box? Same for ATP. Same for enzyme. 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 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
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
Re: [gmx-users] LINCS WARNING
Raymond.nuist wrote: Dear users Here is my problem: I just changed my GMX version from 4.0 to 4.5. But the task was in a Segmentation fault, whileI can mdrun it well in 4.0 environment . Providing an .mdp file and a description of your system would be useful. Here is the error: This suggests nothing beyond physical instability of your system, i.e.: http://www.gromacs.org/Documentation/Terminology/Blowing_Up -Justin Step 1902, time 1.902 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 1057.527961, max 39594.472656 (between atoms 5543 and 5541) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length Step 1902, time 1.902 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 598.238330, max 39421.507812 (between atoms 5544 and 5546) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 2136 2138 32.40.1759 0.1096 0.1096 6874 6869 44.60.1103 0.1082 0.1082 5728 5727 90.00. 0.2223 0.1090 7024 7023 90.00. 0.1591 0.1090 7025 7023 90.00. 2.7347 0.1090 7027 7026 90.00.1118 2.7603 0.1096 7028 7026 90.00.1118 1.7013 0.1096 7029 7030 90.00.1559 0.2336 0.1096 7029 7031 90.00.2080 2.4955 0.1096 8377 8376 41.30.1118 0.1095 0.1096 8385 8382 143.80.1115 2.5694 0.1094 8384 8382 90.00.1115 0.2055 0.1094 5684 5682 42.60.1118 0.1096 0.1096 8383 8382 90.00.1115 0.2720 0.1094 5436 5435 34.80.1113 2.4639 0.1092 5437 5435 90.00.1113 0.8917 0.1092 5438 5435 90.00.1113 0.2059 0.1092 5530 5525 95.50.1637 46.5184 0.1082 5536 5535 90.00. 63.8121 0.1090 5537 5535 110.70. 2.1859 0.1090 5539 5538 90.00.1118 5.2483 0.1096 5540 5538 90.00.1118 0.5557 0.1096 5542 5541 105.90.1118 4.8490 0.1096 5543 5541 90.00.1118 4340.0601 0.1096 5480 5473 54.70.1103 0.1082 0.1082 5545 5544 89.40.1118 18.5327 0.1096 5544 5546 90.00.2399 4321.1011 0.1096 5245 5243 36.60.1113 0.1093 0.1092 2794 2789 90.00.1103 0.3056 0.1082 4160 4158 90.00.1115 0.1108 0.1094 8456 8449 90.00.1103 3.7825 0.1082 7029 7030 90.00.1559 0.2336 0.1096 4520 4513 90.00.1103 0.2065 0.1082 7029 7031 90.00.2080 2.4955 0.1096 7033 7032 90.00.1118 2.6289 0.1096 7034 7032 90.00.1118 0.4015 0.1096 4524 4523 65.10.1113 0.1091 0.1092 10281 10276 68.70.1105 0.1083 0.1083 7041 7038 35.70.1115 0.1094 0.1094 2136 2138 32.40.1759 0.1096 0.1096 10282 10277 90.00.1103 0.1607 0.1082 10288 10287 90.00. 0.3496 0.1090 5544 5546 90.00.2399 4321.1011 0.1096 5544 5545 89.40.1118 18.5327 0.1096 5548 5547 90.00.1118 1.0539 0.1096 5549 5547 48.50.1118 0.1038 0.1096 2800 2799 90.00. 2.8513 0.1090 2801 2799 90.00. 0.6884 0.1090 10291 10290 90.00.1118 0.1451 0.1096 3520 3519 90.00. 1.1565 0.1090 3521 3519 90.00. 0.7086 0.1090 3525 3526 90.00.2190 12.9248 0.1096 3525 3527 90.00.1127 0.1825 0.1096 5494 5493 50.90.1118 0.1038 0.1096 5495 5493 90.00.1118 1.3247 0.1096 8460 8459 90.00.1113 1.3661 0.1092 8461 8459 90.00.1113 0.2465 0.1092 8462 8459 90.00.1113 0.2054 0.1092 3525 3526 90.00.2190 12.9248 0.1096 3525 3527 90.00.1127 0.1825 0.1096 4528 4527 90.00. 1.1331 0.1090 4529 4527 32.80. 0.1132 0.1090 4531 4530 90.00.1118 0.1824 0.1096 4532 4530 40.40.1118 3.0513 0.1096 4535 4533 90.00.1118 0.1212 0.1096 10280 10273 90.00.1103 0.3980 0.1082 6648 6649 90.00.1118 2.0258 0.1096 6653 6651 90.00.1118 1.9735 0.1096 6657 6654 90.00.1115 2.2662 0.1094 4522 4517 46.80.1103 0.1082 0.1082 6646 6645 90.00.1117 1.3712 0.1096 6985 6984 41.00.1118 0.1096 0.1096 3529 3528 90.00.1118 0.1886 0.1096 3530 3528 90.00.1118 0.1834 0.1096 2991 2992 90.00.2281 61.6154 0.1090 2991 2993 90.00.1982 0.3326
Re: [gmx-users] Lincs warning
Moeed wrote: Dear gmx experts, I am having problem doing MD run for a hydrocarbon system. The system contains a stack of Hexane molecules using editconf. The distance between molecuels in the box is more than 30 A. I am wondering why I get large forces (system is blowing up) with this distance!. (LINCS warning) with dt=0.002 Program mdrun, VERSION 4.0.7 Source code file: constr.c, line: 136 Fatal error: Too many LINCS warnings (1053) 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 It seems Fmax, Epot values are reasonable. . In the list archive I read I would say they are not. snip Steepest Descents converged to Fmax 1000 in 30 steps Potential Energy = 4.76092783832156e+05 Maximum force = 9.86600079729483e+02 on atom 3115 Norm of force = 5.33725886931530e+02 You have a reasonable force, but your potential energy is large and positive, indicative strong repulsive forces in your system. snip define = -DPOSRES What are you restraining, and what purpose does it serve? -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/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 WARNING max 597108032.000000 (between atoms 366 and 368) ?
Hi, So many posts and replies on a single issue, and still no exact command lines, nor grompp output, nor gromacs version. Lin, please be aware that such errors only make sense in the context of what you did. You'll have to provide all information that might be related to it. I'm pretty sure that your command lines will reveal the problem, and otherwise the grompp output will. If I have to make a guess, which is all one can do with the information provided, I'd say the PBC is incorrect. Maybe you converted to .pdb format at an intermediary step which is known to remove the PBC in some gromacs versions. Cheers, Tsjerk On Thu, Dec 31, 2009 at 2:47 AM, Mark Abraham mark.abra...@anu.edu.au wrote: Chih-Ying Lin wrote: Hi what does the max max 597108032.00 (between atoms 366 and 368) mean? is it the max force or max length of the system? where is the max force listed? Don't know. max 597108032.00 (between atoms 366 and 368) rms 26394490.00 bonds that rotated more than 30 degrees: what does previous, current mean? is it previous length and current length? Yeah probably. You need to understand what LINCS does to make some sense of this output. It doesn't really matter though. A well-behaved simulation will have none of these warnings. Atoms 366 and 368 are connected by a constraint and unhappy at the start of the simulation. In the output you quote, their distance has gone from under 1nm to a ridiculous number. Look at the region of those atoms in the starting configuration, and work out why. The most likely hypothesis is that some other atom is so close to them that they experienced a massive force, and had massive LJ. Mark Thank you Lin Step 0, time 0 (ps) LINCS WARNING relative constraint deviation after LINCS: max 597108032.00 (between atoms 366 and 368) rms 26394490.00 bonds that rotated more than 30 degrees: *atom 1 atom 2 angle previous, current, constraint length * 26 39 52.0 0.1530 0.1699 0.1530 39 40 69.4 0.1230 0.1423 0.1230 39 41 40.7 0.1330 0.1502 0.1330 75 76 36.0 0.1250 0.1252 0.1250 133 134 69.5 0.1530 0.1937 0.1530 134 135 89.8 0.1470 0.2036 0.1470 344 346 42.4 0.1470 0.2090 0.1470 346 347 42.2 0.1530 0.2141 0.1530 346 359 63.9 0.1530 26006.0332 0.1530 359 360 56.9 0.1230 26006.0469 0.1230 359 361 83.2 0.1330 82898.5859 0.1330 361 362 77.5 0.1000 82845.7109 0.1000 361 363 83.8 0.1470 398710.1875 0.1470 363 364 89.3 0.1530 1909291.8750 0.1530 363 369 85.2 0.1530 393002.8125 0.1530 364 365 90.0 0.1508 31146174. 0.1530 365 366 90.2 0.1544 66925512. 0.1530 366 367 92.7 0.1301 73689816. 0.1250 366 368 87.0 0.1305 74638504. 0.1250 369 370 72.1 0.1230 65978.3203 0.1230 369 371 72.6 0.1330 66864.2812 0.1330 371 372 85.7 0.1000 10685.0596 0.1000 371 373 61.0 0.1470 10685.1035 0.1470 373 374 33.3 0.1530 0.1896 0.1530 373 377 33.5 0.1530 0.1933 0.1530 547 548 90.1 0.1089 0.1358 0.1090 898 900 89.9 0.1530 0.4741 0.1530 -- gmx-users mailing list gmx-us...@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 -- Tsjerk A. Wassenaar, Ph.D. Computational Chemist Medicinal Chemist Neuropharmacologist -- 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 WARNING max 597108032.000000 (between atoms 366 and 368) ?
Chih-Ying Lin wrote: Hi what does the max max 597108032.00 (between atoms 366 and 368) mean? is it the max force or max length of the system? where is the max force listed? Don't know. max 597108032.00 (between atoms 366 and 368) rms 26394490.00 bonds that rotated more than 30 degrees: what does previous, current mean? is it previous length and current length? Yeah probably. You need to understand what LINCS does to make some sense of this output. It doesn't really matter though. A well-behaved simulation will have none of these warnings. Atoms 366 and 368 are connected by a constraint and unhappy at the start of the simulation. In the output you quote, their distance has gone from under 1nm to a ridiculous number. Look at the region of those atoms in the starting configuration, and work out why. The most likely hypothesis is that some other atom is so close to them that they experienced a massive force, and had massive LJ. Mark Thank you Lin Step 0, time 0 (ps) LINCS WARNING relative constraint deviation after LINCS: max 597108032.00 (between atoms 366 and 368) rms 26394490.00 bonds that rotated more than 30 degrees: *atom 1 atom 2 angle previous, current, constraint length * 26 39 52.00.1530 0.1699 0.1530 39 40 69.40.1230 0.1423 0.1230 39 41 40.70.1330 0.1502 0.1330 75 76 36.00.1250 0.1252 0.1250 133134 69.50.1530 0.1937 0.1530 134135 89.80.1470 0.2036 0.1470 344346 42.40.1470 0.2090 0.1470 346347 42.20.1530 0.2141 0.1530 346359 63.90.1530 26006.0332 0.1530 359360 56.90.1230 26006.0469 0.1230 359361 83.20.1330 82898.5859 0.1330 361362 77.50.1000 82845.7109 0.1000 361363 83.80.1470 398710.1875 0.1470 363364 89.30.1530 1909291.8750 0.1530 363369 85.20.1530 393002.8125 0.1530 364365 90.00.1508 31146174. 0.1530 365366 90.20.1544 66925512. 0.1530 366367 92.70.1301 73689816. 0.1250 366368 87.00.1305 74638504. 0.1250 369370 72.10.1230 65978.3203 0.1230 369371 72.60.1330 66864.2812 0.1330 371372 85.70.1000 10685.0596 0.1000 371373 61.00.1470 10685.1035 0.1470 373374 33.30.1530 0.1896 0.1530 373377 33.50.1530 0.1933 0.1530 547548 90.10.1089 0.1358 0.1090 898900 89.90.1530 0.4741 0.1530 -- 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 WARNING max 597108032.000000 (between atoms 366 and 368) ?
Chih-Ying Lin wrote: Hi what does the max max 597108032.00 (between atoms 366 and 368) mean? is it the max force or max length of the system? where is the max force listed? It corresponds to the length between the constrained atoms. Forces are printed to the .trr file if you have set nstfout 0. max 597108032.00 (between atoms 366 and 368) rms 26394490.00 bonds that rotated more than 30 degrees: what does previous, current mean? The constraint length at the previous step and the current one. Judging by the size of these values, it means your system is exploding hopelessly, as the constrained bond is currently at nearly infinite length. -Justin is it previous length and current length? Thank you Lin Step 0, time 0 (ps) LINCS WARNING relative constraint deviation after LINCS: max 597108032.00 (between atoms 366 and 368) rms 26394490.00 bonds that rotated more than 30 degrees: *atom 1 atom 2 angle previous, current, constraint length * 26 39 52.00.1530 0.1699 0.1530 39 40 69.40.1230 0.1423 0.1230 39 41 40.70.1330 0.1502 0.1330 75 76 36.00.1250 0.1252 0.1250 133134 69.50.1530 0.1937 0.1530 134135 89.80.1470 0.2036 0.1470 344346 42.40.1470 0.2090 0.1470 346347 42.20.1530 0.2141 0.1530 346359 63.90.1530 26006.0332 0.1530 359360 56.90.1230 26006.0469 0.1230 359361 83.20.1330 82898.5859 0.1330 361362 77.50.1000 82845.7109 0.1000 361363 83.80.1470 398710.1875 0.1470 363364 89.30.1530 1909291.8750 0.1530 363369 85.20.1530 393002.8125 0.1530 364365 90.00.1508 31146174. 0.1530 365366 90.20.1544 66925512. 0.1530 366367 92.70.1301 73689816. 0.1250 366368 87.00.1305 74638504. 0.1250 369370 72.10.1230 65978.3203 0.1230 369371 72.60.1330 66864.2812 0.1330 371372 85.70.1000 10685.0596 0.1000 371373 61.00.1470 10685.1035 0.1470 373374 33.30.1530 0.1896 0.1530 373377 33.50.1530 0.1933 0.1530 547548 90.10.1089 0.1358 0.1090 898900 89.90.1530 0.4741 0.1530 -- 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/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 Warning
Samik Bhattacharya wrote: Hi all, i ma simulating a membrane protein, in which i am facing a problem in the equilibration step. in the NVT equilibration when i am running the mdrun command i am getting a msg like Program mdrun, VERSION 4.0.5 Source code file: constr.c, line: 136 Fatal error: Too many LINCS warnings (1966) 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 i cant understand how to fix the problem. where actually lies the error? is it in the mdp file i am using? some suggestions will be really helpful in this regard. Thank you all for the help in advance. http://oldwiki.gromacs.org/index.php/Errors#LINCS.2FSETTLE.2FSHAKE_warnings 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/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 Warning
--- On Wed, 15/7/09, Mark Abraham mark.abra...@anu.edu.au wrote: From: Mark Abraham mark.abra...@anu.edu.au Subject: Re: [gmx-users] Lincs Warning To: Discussion list for GROMACS users gmx-users@gromacs.org Date: Wednesday, 15 July, 2009, 5:23 PM Samik Bhattacharya wrote: Hi all, i ma simulating a membrane protein, in which i am facing a problem in the equilibration step. in the NVT equilibration when i am running the mdrun command i am getting a msg like Program mdrun, VERSION 4.0.5 Source code file: constr.c, line: 136 Fatal error: Too many LINCS warnings (1966) 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 i cant understand how to fix the problem. where actually lies the error? is it in the mdp file i am using? some suggestions will be really helpful in this regard. Thank you all for the help in advance. http://oldwiki.gromacs.org/index.php/Errors#LINCS.2FSETTLE.2FSHAKE_warnings Thanks You Mark. for your help... perhaps the error lies lies in EM step which converged very early in previous steps. when i was running EM for 5000 steps it was converging in less than 50 steps. and was showing a msg like Stepsize too small, or no change in energy. Converged to machine precision, but not to the requested precision would doule precision remove this problem? again i cant rule out the system blowing up error. in that case how to increase 1-4 interaction? looking forward for your valuable comments. Thank You Shamik Yahoo! recommends that you upgrade to the new and safer Internet Explorer 8. http://downloads.yahoo.com/in/internetexplorer/___ 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 Warning
Samik Bhattacharya wrote: --- On *Wed, 15/7/09, Mark Abraham /mark.abra...@anu.edu.au/* wrote: From: Mark Abraham mark.abra...@anu.edu.au Subject: Re: [gmx-users] Lincs Warning To: Discussion list for GROMACS users gmx-users@gromacs.org Date: Wednesday, 15 July, 2009, 5:23 PM Samik Bhattacharya wrote: Hi all, i ma simulating a membrane protein, in which i am facing a problem in the equilibration step. in the NVT equilibration when i am running the mdrun command i am getting a msg like Program mdrun, VERSION 4.0.5 Source code file: constr.c, line: 136 Fatal error: Too many LINCS warnings (1966) 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 i cant understand how to fix the problem.. where actually lies the error? is it in the mdp file i am using? some suggestions will be really helpful in this regard. Thank you all for the help in advance. http://oldwiki.gromacs.org/index.php/Errors#LINCS.2FSETTLE.2FSHAKE_warnings Thanks You Mark. for your help... perhaps the error lies lies in EM step which converged very early in previous steps. when i was running EM for 5000 steps it was converging in less than 50 steps. and was showing a msg like Stepsize too small, or no change in energy. Converged to machine precision, but not to the requested precision would doule precision remove this problem? again i cant rule out the system blowing up error. in that case how to increase 1-4 interaction? looking forward for your valuable comments. Thank You Shamik The question is not when energy minimization converged, but whether or not it converged to an appropriate value of Epot and Fmax. What values did you obtain? -Justin Looking for local information? Find it on Yahoo! Local http://in.rd.yahoo.com/tagline_local_1/*http://in.local.yahoo.com/ ___ 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 -- 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 Warning
--- On Thu, 16/7/09, Justin A. Lemkul jalem...@vt.edu wrote: From: Justin A. Lemkul jalem...@vt.edu Subject: Re: [gmx-users] Lincs Warning To: Discussion list for GROMACS users gmx-users@gromacs.org Date: Thursday, 16 July, 2009, 7:30 AM Samik Bhattacharya wrote: --- On *Wed, 15/7/09, Mark Abraham /mark.abra...@anu.edu.au/* wrote: From: Mark Abraham mark.abra...@anu.edu.au Subject: Re: [gmx-users] Lincs Warning To: Discussion list for GROMACS users gmx-users@gromacs.org Date: Wednesday, 15 July, 2009, 5:23 PM Samik Bhattacharya wrote: Hi all, i ma simulating a membrane protein, in which i am facing a problem in the equilibration step. in the NVT equilibration when i am running the mdrun command i am getting a msg like Program mdrun, VERSION 4.0.5 Source code file: constr.c, line: 136 Fatal error: Too many LINCS warnings (1966) 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 i cant understand how to fix the problem.. where actually lies the error? is it in the mdp file i am using? some suggestions will be really helpful in this regard. Thank you all for the help in advance. http://oldwiki.gromacs.org/index.php/Errors#LINCS.2FSETTLE.2FSHAKE_warnings Thanks You Mark. for your help... perhaps the error lies lies in EM step which converged very early in previous steps. when i was running EM for 5000 steps it was converging in less than 50 steps. and was showing a msg like Stepsize too small, or no change in energy. Converged to machine precision, but not to the requested precision would doule precision remove this problem? again i cant rule out the system blowing up error. in that case how to increase 1-4 interaction? looking forward for your valuable comments. Thank You Shamik The question is not when energy minimization converged, but whether or not it converged to an appropriate value of Epot and Fmax. What values did you obtain? -Justin hi, Justin..good to hear from you again... the values i got are given below (taken from the log file): Stepsize too small, or no change in energy. Converged to machine precision, but not to the requested precision Fmax 1000 Double precision normally gives you higher accuracy. You might need to increase your constraint accuracy, or turn off constraints alltogether (set constraints = none in mdp file) Steepest Descents converged to machine precision in 31 steps, but did not reach the requested Fmax 1000. Potential Energy = -1.0261834e+23 Maximum force = 4.9815813e+24 on atom 169274 Norm of force = 6.4473938e+21 M E G A - F L O P S A C C O U N T I N G RF=Reaction-Field FE=Free Energy SCFE=Soft-Core/Free Energy T=Tabulated W3=SPC/TIP3p W4=TIP4p (single or pairs) NF=No Forces Computing: M-Number M-Flops % Flops --- LJ 30.494607 1006.322 0.1 Coul(T) 24.286588 1020.037 0.1 Coul(T) [W3] 0.205871 25.734 0.0 Coul(T) + LJ 13.019726 716.085 0.0 Coul(T) + LJ [W3] 8.396028 1158.652 0.1 Coul(T) + LJ [W3-W3] 3018.437056 1153042.955 71.1 Outer nonbonded loop 318.129558 3181.296 0.2 1,4 nonbonded interactions 0.204724 18.425 0.0 Calc Weights 229.781517 8272.135 0.5 Spread Q Bspline 4902.005696 9804.011 0.6 Gather F Bspline 4902.005696 58824.068 3.6 3D-FFT 21969.184718 175753.478 10.8 Solve PME 234.707200 15021.261 0.9 NS-Pairs 8380.302391 175986.350 10.8 Reset In Box 25.604636 76.814 0.0 Shift-X 76.593746 459.562 0.0 CG-CoM 76.593839 229.782 0.0 Bonds 0.247597 14.608 0.0 Angles 0.306280 51.455 0..0 Propers 0.117800 26.976 0..0 Impropers 0.043276 9.001 0.0 RB-Dihedrals 0.092256 22.787 0.0 Virial 76.595234 1378.714 0.1 Settle 50.895614 16439.283 1.0 --- Total
RE: [gmx-users] Lincs Warning
Maximum force = 4.9815813e+24 on atom 169274 You should have a look at that atom, that is a large force. ___ 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 warning
XAvier Periole wrote: Dears, I am experiencing some problems running a few proteins in water (GROMOS43a1/SPC) with gmx-4.0.4 using 32 CPUs. After some ns lincs warnings appear and eventually the simulation crashes dues to too many lincs warnings. When restarting the simulation feeding -cpi md.cpt to mdrun the simulation restarts fine and no lincs warning are reported on the same portion of the simulation. The simulation runs again for some ns and the same happens: new lincs warning appear and eventually the simulation crashes again. Any explanation for this? Any solution? Check out 4.0.5 release notes? Check out 4.0.5? Mark ___ 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] lincs warning
On Jun 3, 2009, at 9:51 AM, Mark Abraham wrote: XAvier Periole wrote: Dears, I am experiencing some problems running a few proteins in water (GROMOS43a1/SPC) with gmx-4.0.4 using 32 CPUs. After some ns lincs warnings appear and eventually the simulation crashes dues to too many lincs warnings. When restarting the simulation feeding -cpi md.cpt to mdrun the simulation restarts fine and no lincs warning are reported on the same portion of the simulation. The simulation runs again for some ns and the same happens: new lincs warning appear and eventually the simulation crashes again. Any explanation for this? Any solution? Check out 4.0.5 release notes? Check out 4.0.5? Yes. Nothing that seem to matter to these lincs warnings! Mark ___ 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] lincs warning
Hi XAvier, Do you use virtual sites? I've seen this when I used virtual sites, large time steps and a system that probably wasn't equilibrated enough. Ran. XAvier Periole wrote: Dears, I am experiencing some problems running a few proteins in water (GROMOS43a1/SPC) with gmx-4.0.4 using 32 CPUs. After some ns lincs warnings appear and eventually the simulation crashes dues to too many lincs warnings. When restarting the simulation feeding -cpi md.cpt to mdrun the simulation restarts fine and no lincs warning are reported on the same portion of the simulation. The simulation runs again for some ns and the same happens: new lincs warning appear and eventually the simulation crashes again. Any explanation for this? Any solution? Best, XAvier. ___ 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 thewww interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] lincs warning
On Jun 3, 2009, at 10:01 AM, Ran Friedman wrote: Hi XAvier, Do you use virtual sites? I've seen this when I used virtual sites, No virtual sites. large time steps and a system that probably wasn't equilibrated enough. time step 2 fs and a system totally equilibrated, nothing there. I would have considered this if the warning were reproduced when restarting the simulation. It seems more that it is a loss of accuracy due to communication between CPUs ? XAvier. Ran. XAvier Periole wrote: Dears, I am experiencing some problems running a few proteins in water (GROMOS43a1/SPC) with gmx-4.0.4 using 32 CPUs. After some ns lincs warnings appear and eventually the simulation crashes dues to too many lincs warnings. When restarting the simulation feeding -cpi md.cpt to mdrun the simulation restarts fine and no lincs warning are reported on the same portion of the simulation. The simulation runs again for some ns and the same happens: new lincs warning appear and eventually the simulation crashes again. Any explanation for this? Any solution? Best, XAvier. ___ 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 thewww interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] lincs warning
XAvier Periole skrev: On Jun 3, 2009, at 10:01 AM, Ran Friedman wrote: Hi XAvier, Do you use virtual sites? I've seen this when I used virtual sites, No virtual sites. large time steps and a system that probably wasn't equilibrated enough. time step 2 fs and a system totally equilibrated, nothing there. I would have considered this if the warning were reproduced when restarting the simulation. It seems more that it is a loss of accuracy due to communication between CPUs ? If you use dynamic load balancing then you are sacrificing binary reproducibility. Because of this, and the chaotic nature of MD, the error will likely not occur at the same point in your continuation. Still, the source of the error persists and is what demands attention I'd say. XAvier. Ran. XAvier Periole wrote: Dears, I am experiencing some problems running a few proteins in water (GROMOS43a1/SPC) with gmx-4.0.4 using 32 CPUs. After some ns lincs warnings appear and eventually the simulation crashes dues to too many lincs warnings. When restarting the simulation feeding -cpi md.cpt to mdrun the simulation restarts fine and no lincs warning are reported on the same portion of the simulation. The simulation runs again for some ns and the same happens: new lincs warning appear and eventually the simulation crashes again. Any explanation for this? Any solution? Best, XAvier. ___ 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 thewww interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ 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 thewww interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- --- Erik Marklund, PhD student Laboratory of Molecular Biophysics, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596,75124 Uppsala, Sweden phone:+46 18 471 4537fax: +46 18 511 755 er...@xray.bmc.uu.sehttp://xray.bmc.uu.se/molbiophys ___ 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] lincs warning
On Jun 3, 2009, at 10:58 AM, Giovanni Bussi wrote: Dear Xavier, With the default flag for pbc (periodic_molecules=no) you may end up in lincs problem if an atom of the protein becomes too close to the image of another atom of the protein. If this is your case, use periodic_molecules=yes, or enlarge the solvation cell. Thanks, I have however a very large water box and no problem there I believe. Hope this helps, Giovanni On Wed, Jun 3, 2009 at 10:48 AM, Erik Marklund er...@xray.bmc.uu.se wrote: XAvier Periole skrev: On Jun 3, 2009, at 10:01 AM, Ran Friedman wrote: Hi XAvier, Do you use virtual sites? I've seen this when I used virtual sites, No virtual sites. large time steps and a system that probably wasn't equilibrated enough. time step 2 fs and a system totally equilibrated, nothing there. I would have considered this if the warning were reproduced when restarting the simulation. It seems more that it is a loss of accuracy due to communication between CPUs ? If you use dynamic load balancing then you are sacrificing binary reproducibility. Because of this, and the chaotic nature of MD, the error will likely not occur at the same point in your continuation. Still, the source of the error persists and is what demands attention I'd say. XAvier. Ran. XAvier Periole wrote: Dears, I am experiencing some problems running a few proteins in water (GROMOS43a1/SPC) with gmx-4.0.4 using 32 CPUs. After some ns lincs warnings appear and eventually the simulation crashes dues to too many lincs warnings. When restarting the simulation feeding -cpi md.cpt to mdrun the simulation restarts fine and no lincs warning are reported on the same portion of the simulation. The simulation runs again for some ns and the same happens: new lincs warning appear and eventually the simulation crashes again. Any explanation for this? Any solution? Best, XAvier. ___ 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 thewww interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ 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 thewww interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- --- Erik Marklund, PhD student Laboratory of Molecular Biophysics, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596,75124 Uppsala, Sweden phone:+46 18 471 4537fax: +46 18 511 755 er...@xray.bmc.uu.sehttp://xray.bmc.uu.se/molbiophys ___ 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] lincs warning
On Jun 3, 2009, at 10:48 AM, Erik Marklund wrote: XAvier Periole skrev: On Jun 3, 2009, at 10:01 AM, Ran Friedman wrote: Hi XAvier, Do you use virtual sites? I've seen this when I used virtual sites, No virtual sites. large time steps and a system that probably wasn't equilibrated enough. time step 2 fs and a system totally equilibrated, nothing there. I would have considered this if the warning were reproduced when restarting the simulation. It seems more that it is a loss of accuracy due to communication between CPUs ? If you use dynamic load balancing then you are sacrificing binary reproducibility. Because of this, and the chaotic nature of MD, the error will likely not occur at the same point in your continuation. Still, the source of the error persists and is what demands attention I'd say. Well starting from a cpt file, I would expect reproducibility at the difference that the decomposition over CPUs might be refreshed. It might be but I am still favoring a communication issue. I am now testing the effect of using -rdd and -rcon on the LINCS warnings. XAvier. Ran. XAvier Periole wrote: Dears, I am experiencing some problems running a few proteins in water (GROMOS43a1/SPC) with gmx-4.0.4 using 32 CPUs. After some ns lincs warnings appear and eventually the simulation crashes dues to too many lincs warnings. When restarting the simulation feeding -cpi md.cpt to mdrun the simulation restarts fine and no lincs warning are reported on the same portion of the simulation. The simulation runs again for some ns and the same happens: new lincs warning appear and eventually the simulation crashes again. Any explanation for this? Any solution? Best, XAvier. ___ 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 thewww interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ 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 thewww interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- --- Erik Marklund, PhD student Laboratory of Molecular Biophysics, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596,75124 Uppsala, Sweden phone:+46 18 471 4537fax: +46 18 511 755 er...@xray.bmc.uu.sehttp://xray.bmc.uu.se/molbiophys ___ 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] LINCS warning
serdar durdagi wrote: Dear all, I am making drg+lipid simulations with gmx. From the 9 series of experiments all of them worked fine for 250 ps equilubration run. However, when I start the real simulation, 4 of them stopped after 300 ps (I have setted the simualtion time to 2.5 ns). It complains the LINCS warning. relative constraint deviation after LINC. All the systems are very similar, just different conformations of drug. So, I can not see any reason why some of them are working fine and some of them not. Those different conformations may have different (bad) interactions with the other elements of your system. Having described nothing about your preparation, minimization, or equilibration scheme, that's about the best I can see to offer. View the trajectory and see where things are starting to explode. That will give you a hint as to where the problem lies. There are hundreds of posts about LINCS warnings in the mailing list archive, as well as the following wiki site: http://wiki.gromacs.org/index.php/blowing_up These sources should provide you with many things to try. One final note: Depending on the size of these drug molecules, it may not be appropriate to couple them to their own temperature bath. Insufficient degrees of freedom (i.e., coupling a few ions to their own bath) can lead to the same type of weird, random explosions. For more information, again, consult the wiki: http://wiki.gromacs.org/index.php/Thermostats -Justin I attached the last steps of log file and used mdp file. Thank you very much in advance for solution suggestions. Serdar Durdagi title = CB1_conf_a MD cpp = /usr/bin/cpp constraints = all-bonds integrator = md dt = 0.002 ; ps ! nsteps = 125 nstcomm = 1 nstxout = 500 nstvout = 0 nstfout = 0 nstlog = 500 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 ; Berendsen temperature coupling is on Tcoupl = berendsen tau_t = 0.1 0.1 0.1 tc-grps = DPP C6 SOL ref_t = 300 300 300 ; Pressure coupling is on Pcoupl = no tau_p = 0.5 compressibility = 4.5e-5 ref_p = 1.0 Generate velocities is on at 300 K. gen_vel = yes gen_temp = 300.0 gen_seed = 173529 Step Time Lambda 166500 333.00.0 Rel. Constraint Deviation: Maxbetween atoms RMS Before LINCS 0.006301 4163 4164 0.001222 After LINCS 0.000144 27 28 0.06 Energies (kJ/mol) AngleProper Dih. Ryckaert-Bell. Improper Dih. LJ-14 1.08817e+042.92391e+035.33679e+033.48481e+021.18752e+03 Coulomb-14LJ (SR)LJ (LR) Coulomb (SR) Coul. recip. 1.33953e+04 -6.78212e+03 -2.28400e+03 -1.91715e+05 -1.13117e+05 PotentialKinetic En. Total EnergyTemperature Pressure (bar) -2.79825e+054.07337e+04 -2.39091e+053.03482e+02 -3.62649e+02 Step Time Lambda 167000 334.00.0 Rel. Constraint Deviation: Maxbetween atoms RMS Before LINCS 0.006221 2094 2095 0.001243 After LINCS 0.50 27 28 0.04 Energies (kJ/mol) AngleProper Dih. Ryckaert-Bell. Improper Dih. LJ-14 1.11706e+042.98252e+035.26699e+033.75113e+021.34753e+03 Coulomb-14LJ (SR)LJ (LR) Coulomb (SR) Coul. recip. 1.30631e+04 -7.42424e+03 -2.27672e+03 -1.89582e+05 -1.12967e+05 PotentialKinetic En. Total EnergyTemperature Pressure (bar) -2.78044e+053.95852e+04 -2.38459e+052.94925e+02 -2.05298e+02 Step Time Lambda 167500 335.00.0 Rel. Constraint Deviation: Maxbetween atoms RMS Before LINCS 0.005474693694 0.001211 After LINCS 0.78 27 28 0.04 Energies (kJ/mol) AngleProper Dih. Ryckaert-Bell. Improper Dih. LJ-14 1.10570e+042.92074e+035.41756e+033.52792e+021.27318e+03 Coulomb-14LJ (SR)LJ (LR) Coulomb (SR) Coul. recip. 1.29374e+04 -7.77397e+03 -2.27790e+03 -1.89057e+05 -1.13016e+05 PotentialKinetic En. Total EnergyTemperature Pressure (bar) -2.78166e+054.01726e+04 -2.37993e+052.99302e+02 -2.13536e+02 Step 167969, time 335.938 (ps) LINCS WARNING relative constraint deviation after LINCS: max inf (between atoms 3 and 4) rms inf bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 2 3 31.70.1530 0.1802 0.1530 3 4 71.90.1530
RE: [gmx-users] LINCS WARNING
I am runing a MD of protein. Now I see some warning message on screen,I don't know how to understand it , Could somebody tell me about it? Thank you very much! It means that the bond between the two atoms listed there is moving too far in each time step. The reason for that problem can greatly vary. What it does mean is that something is wrong, either with the parameters or interactions in that region of the simulation, the settings used for running the simulation, or the structure in that region. Perform a search of the emailing list using that error message, and you will come up with a significant number of emails explaining it further, solutions etc. Such as these: http://www.gromacs.org/pipermail/gmx-users/2003-May/005335.html http://www.gromacs.org/pipermail/gmx-users/2006-March/020477.html http://www.gromacs.org/pipermail/gmx-users/2006-July/022578.html Plus many, many more. Catch ya, Dr. Dallas Warren Lecturer Department of Pharmaceutical Biology and Pharmacology Victorian College of Pharmacy, Monash University 381 Royal Parade, Parkville VIC 3010 [EMAIL PROTECTED] +61 3 9903 9524 - When the only tool you own is a hammer, every problem begins to resemble a nail. ___ 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 WARNING
Qiang Zhong wrote: Hellow : I am runing a MD of protein. Now I see some warning message on screen,I don't know how to understand it , Could somebody tell me about it? Thank you very much! First, consider what LINCS does. Then consider what could make LINCS unhappy with the correspondence between its inputs and outputs. Then consider what could cause that. Yes, MD is not meant to be easy. 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 warning
Dear all, I have a query, 1. Are two trajectories comparable if each one of them has been run in a different version of gromacs? Eg, v3.2 and v3.3. Define comparable. If you mean are they sampling the same thermodynamic ensemble, then the answer is yes if you used the same algorithms. If you mean are they numerically identical, the answer is no. Round-off errors from different order of summation, etc. will cause tiny differences that magnify chaotically. 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 warning
Hi everyone, I'm having trouble with performing 1 ns simulations on a 318 residue long protein with 'mdrun'. The run.log file, included at the end of this message, gives a 'LINCS warning' within a minute or two after the simulation begins: Step 148, time 0.296 (ps) LINCS WARNING relative constraint deviation after LINCS: max 0.151505 (between atoms 4353 and 4355) rms 0.002175 bonds that rotated more than 60 degrees: In plain English, this means the bond or angle constraints implemented with the LINCS algorithm are having to be enforced after very large deviations. This suggests that there is something numerically unstable going on. Visualising the trajectory is always a good idea at this point, as it can suggest whether the whole world is exploding (re-visit the preparation protocol) or just part of it (be more cunning). I've have been minimizing the structure of the protein prior to trying to perform the simulation (no problems here). Also, when I use 'grompp' to produce a .tpr file for a 1 ns MD simulation with the minimized structure, I have no problems with this either. The .mdp file that is fed into the .tpr file will work with different protein structures (single residue mutants) without incident. So, it would appear that the .mdp file used to compile the .tpr file is working. Yes... the .mdp file describes the conduct of the simulation, the .top file describes the topology of system, and the structure (.gro) file describes the original conformation. All three are combined to produce the .tpr file. There are some constraints on the three, but subject to those constraints you can swap different .mdp/.top/.gro files. What is really puzzling to me is that the simulation will sometimes run properly and sometimes it won't even though it would appear that I use the exact same .gro file. Does this sound familiar to anyone? There is more needed to prepare a system for MD than energy minimization to relieve bad contacts. Read any MD paper and they will describe some kind of regime for generating initial velocities and heating the system to the required temperature, and then leave it to sit for a while. Often temperatures will be equilibrated in NVT, before relaxing to NPT when that ensemble is desired for the production calculation. Since you don't describe doing this, my guess is that you are not doing it (well enough). 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 Warning with MDRUN - Segmentation Fault
Gaurav Chopra wrote: Hi I am getting the following error with mdrun. I have done a few things but the system complains of 1-4 interactions and gives LINCS warning if the constraints are not turned off in the mdp file. I also changed the fudgeQQ = 1.0 (instead of 0.5) in ffoplsaa.itp and then did mdrun but I get 1-4 interaction table size error and then LINCS warning. The output of mdrun for one of these peptides is as follows. I am working on normal mode decoys of each peptide and many of the decoys have no problems with mdrun but some gives this error and Segmentation Fault. Please advice. you need to minimize better, but if your structures are really bad it won't help either (e.g. when you have a sidechain sticking through a ring) -- David. David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ___ 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 Warning with MDRUN - Segmentation Fault
On Mon, 17 Apr 2006 00:07:29 -0700 Gaurav Chopra [EMAIL PROTECTED] wrote: Hi I am getting the following error with mdrun. I have done a few things but the system complains of 1-4 interactions and gives LINCS warning if the constraints are not turned off in the mdp file. I also changed the fudgeQQ = 1.0 (instead of 0.5) in ffoplsaa.itp and then did mdrun but I get 1-4 interaction table size error and then LINCS warning. The output of mdrun for one of these peptides is as follows. I am working on normal mode decoys of each peptide and many of the decoys have no problems with mdrun but some gives this error and Segmentation Fault. Please advice. The lincs warnning are on water molecules isn't it ??? XAvier ___ 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 Warning using mdrun
Gaurav Chopra wrote: Hi I get the following error when using mdrun for a protein in solution. I have checked the structure and everything looks fine to me. Could you suggested anything else I could do. Step -2, time -0.004 (ps) LINCS WARNING relative constraint deviation after LINCS: max 0.126305 (between atoms 892 and 894) rms 0.007000 bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 898899 41.60.1015 0.0997 0.1010 898900 38.10.1038 0.0984 0.1010 starting mdrun 'HEADER Output set 125 with rmsf= .982 of 1nkd.cl_nH_tir.pdb in water' 10 steps,200.0 ps. Step 0, time 0 (ps) LINCS WARNING relative constraint deviation after LINCS: max 3.372058 (between atoms 894 and 895) rms 0.239340 bonds that rotated more than 30 degrees: Thanks gaurav ___ 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 Hi Gaurav, what is your stepsize during the simulation? what is constrained? And have you run a minimization before starting the simulation? hear from you soon Steffen -- Dipl.-Chem. Steffen Wolf Department of Biophysics University of Bochum ND 04/67 44780 Bochum Germany ___ 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 Warning using mdrun
Gaurav Chopra wrote: Hi I get the following error when using mdrun for a protein in solution. I have checked the structure and everything looks fine to me. Could you suggested anything else I could do. How did you energy minimze your structure? What was the output of mdrun during energy minization, especially the last line with Fmax, Epot etc.? I should look like this: Step= 48, Dmax= 1.1e-02 nm, Epot= -1.45545e+06 Fmax= 5.58480e+05, atom= 78754 Step= 49, Dmax= 1.4e-02 nm, Epot= -1.45551e+06 Fmax= 8.80803e+03, atom= 13032 Step= 50, Dmax= 1.7e-02 nm, Epot= -1.45574e+06 Fmax= 1.60758e+04, atom= 13032 Jochen -- Jochen Hub Max Planck Institute for Biophysical Chemistry Computational biomolecular dynamics group Am Fassberg 11 D-37077 Goettingen, Germany Email: jhub[at]gwdg.de ___ 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
