From: NG HUI WEN Sent: Sunday, February 19, 2012 1:19 PM To: gmx-users@gromacs.org Subject: Distance Restraints on Protein - possible at all?
Dear gmxusers, I have been trying to apply distance restraints on my protein but have been unsuccessful thus far. I have consulted the user forum previously and with some much-appreciated help I have managed to get my simulation (with distance restraints applied) to run. However, the joy did not last long as the simulation crashed very quickly (after ~40-50ps). Below is an account of the attempts I made. Please bear with me as it is quite lenghty. I have tried to resolve the problem (but all to no avail) by : a)changing the distance restraint group from CA to backbone - in case the protein is too floppy b)fc from 10000 to 1000 (default) to 0 - in order to check if the problem comes from the strenght of restraints Below sum up what I had done: 1) prepare disre.itp file genrestr -f posre_NVT_rep1.gro -o ca_disre.itp -disre 2) mdp looks: title = NPT define = -DDISRES integrator = md nsteps = 500000 dt = 0.002 nstxout = 50000 nstvout = 50000 nstenergy = 2500 nstlog = 500 nstxtcout = 50000 continuation = yes constraint_algorithm = lincs constraints = all-bonds lincs_iter = 1 lincs_order = 4 ns_type = grid nstlist = 10 rlist = 1.2 rcoulomb = 1.2 rvdw = 1.2 coulombtype = PME pme_order = 4 fourierspacing = 0.12 tcoupl = v-rescale tc-grps = Protein POPC WATER_SOL_CL tau_t = 0.1 0.1 0.1 ref_t = 310 310 310 pcoupl = Parrinello-Rahman pcoupltype = semiisotropic tau_p = 1.0 ref_p = 1.0 1.0 compressibility = 4.5e-5 4.5e-5 pbc = xyz DispCorr = EnerPres gen_vel = no nstcomm = 10 comm-mode = Linear comm-grps = Protein_POPC WATER_SOL_CL energygrps = Protein POPC WATER_SOL_CL ; DISRE parameters disre = simple disre-fc = (i)10000/ (ii)1000 / (iii) 0 3) top file looks like this: ; Include forcefield parameters #include "gromos53a6_lipid.ff/forcefield.itp" ;Include Protein Topology #include "A2a.itp" ; Include Position restraint file #ifdef DISRES #include "ca_disre.itp" #endif ; #ifdef POSRES #include "posre.itp" #endif ; ;Include POPC topology #include "popc.itp" #ifdef LIPID_POSRES #include "lipid_posre.itp" #endif ;Include water topology #include "gromos53a6_lipid.ff/spc.itp" #ifdef POSRES_WATER ; Position restraint for each water oxygen [ position_restraints ] ; i funct fcx fcy fcz 1 1 1000 1000 1000 #endif ; Include topology for ions #include "gromos53a6_lipid.ff/ions.itp" [ system ] ; Name POPC and protein in water [ molecules ] ; Compound #mols Protein_chain_X 1 POPC 327 SOL 24767 CL 11 4) prepare .tpr file grompp -f NPT_disres.mdp -c posre_NPT_rep1.gro -n index.ndx -p merged.top -t posre_NPT_rep1.cpt -o disre.tpr 5) mdrun mdrun-mpi -v -s disre.tpr -deffnm disre -pd The following are snippets of the output and log file before the simulations blew up: i)fc= 10000 step 21300, will finish Wed Feb 15 11:07:18 2012 step 21400, will finish Wed Feb 15 11:08:38 2012 Step 21481, time 42.962 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.007728, max 0.339710 (between atoms 9 and 11) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length Step 21482, time 42.964 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.022906, max 0.865028 (between atoms 12 and 16) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 16 17 31.6 0.1212 0.1447 0.1230 12 16 104.7 0.1266 0.0207 0.1530 9 11 110.7 0.0878 0.0397 0.1330 Wrote pdb files with previous and current coordinates Step 21483, time 42.966 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.009368, max 0.641094 (between atoms 9 and 11) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 1 2 33.3 0.0928 0.0961 0.1000 18 20 34.2 0.1474 0.1635 0.1470 16 18 60.0 0.1842 0.1310 0.1330 16 17 64.8 0.1447 0.1264 0.1230 14 15 30.4 0.0979 0.1525 0.1530 11 15 77.5 0.2435 0.1147 0.1470 11 12 34.5 0.2609 0.1633 0.1470 9 11 95.3 0.0397 0.2183 0.1330 Wrote pdb files with previous and current coordinates Step 21484, time 42.968 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.013088, max 0.518530 (between atoms 12 and 16) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 1 2 40.0 0.0961 0.0952 0.1000 18 19 59.6 0.0996 0.0782 0.1000 .... ii) fc= 1000 (default) step 21200, will finish Thu Feb 16 02:22:10 2012 step 21300, will finish Thu Feb 16 02:22:09 2012 step 21400, will finish Thu Feb 16 02:22:07 2012 Step 21481, time 42.962 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.007728, max 0.339710 (between atoms 9 and 11) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length Step 21482, time 42.964 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.022906, max 0.865028 (between atoms 12 and 16) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 16 17 31.6 0.1212 0.1447 0.1230 12 16 104.7 0.1266 0.0207 0.1530 9 11 110.7 0.0878 0.0397 0.1330 Wrote pdb files with previous and current coordinates Step 21483, time 42.966 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.009368, max 0.641094 (between atoms 9 and 11) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 1 2 33.3 0.0928 0.0961 0.1000 18 20 34.2 0.1474 0.1635 0.1470 16 18 60.0 0.1842 0.1310 0.1330 16 17 64.8 0.1447 0.1264 0.1230 14 15 30.4 0.0979 0.1525 0.1530 11 15 77.5 0.2435 0.1147 0.1470 11 12 34.5 0.2609 0.1633 0.1470 9 11 95.3 0.0397 0.2183 0.1330 Wrote pdb files with previous and current coordinates ... ... ... log file at the start and just before the simulation blew up: Started mdrun on node 0 Wed Feb 15 14:46:26 2012 Step Time Lambda 0 0.00000 0.00000 Grid: 15 x 15 x 16 cells Energies (kJ/mol) Angle G96Angle Proper Dih. Ryckaert-Bell. Improper Dih. 3.62720e+04 5.42463e+03 1.35029e+04 1.73286e+04 3.49678e+03 LJ-14 Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) 1.12718e+04 7.18682e+04 8.12244e+04 -7.18252e+03 -1.27427e+06 Coul. recip. Dis. Rest. D.R.Viol. (nm) Potential Kinetic En. -3.89615e+05 0.00000e+00 0.00000e+00 -1.43068e+06 2.42524e+05 Total Energy Temperature Pres. DC (bar) Pressure (bar) Constr. rmsd -1.18815e+06 3.08494e+02 -1.97177e+02 5.79670e+02 1.01684e-05 Step Time Lambda 500 1.00000 0.00000 Energies (kJ/mol) Angle G96Angle Proper Dih. Ryckaert-Bell. Improper Dih. 3.59484e+04 5.33007e+03 1.32268e+04 1.70061e+04 3.50560e+03 LJ-14 Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) 1.10240e+04 7.14613e+04 8.03669e+04 -7.03778e+03 -1.26659e+06 Coul. recip. Dis. Rest. D.R.Viol. (nm) Potential Kinetic En. -3.88952e+05 5.48165e+01 9.39514e+00 -1.42466e+06 2.43342e+05 Total Energy Temperature Pres. DC (bar) Pressure (bar) Constr. rmsd -1.18131e+06 3.09534e+02 -1.89310e+02 4.99800e+02 1.05856e-05 ... ... Step Time Lambda 21000 42.00000 0.00000 Energies (kJ/mol) Angle G96Angle Proper Dih. Ryckaert-Bell. Improper Dih. 3.62118e+04 5.30282e+03 1.34838e+04 1.83737e+04 3.33814e+03 LJ-14 Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) 1.12261e+04 6.97720e+04 8.28599e+04 -6.87470e+03 -1.25607e+06 Coul. recip. Dis. Rest. D.R.Viol. (nm) Potential Kinetic En. -3.87420e+05 4.27582e+01 6.98584e+00 -1.40975e+06 2.44245e+05 Total Energy Temperature Pres. DC (bar) Pressure (bar) Constr. rmsd -1.16551e+06 3.10684e+02 -1.80638e+02 -5.00713e+02 1.04526e-05 Large VCM(group Protein_POPC): 73.33204, 29.76558, -12.48454, Temp-cm: 2.95863e+05 Large VCM(group Water_SOL_CL): -46.46529, -18.86033, 7.91055, Temp-cm: 3.35241e+04 iii) fc = 0 The end of the log file looks: Step Time Lambda 29000 58.00000 0.00000 Energies (kJ/mol) Angle G96Angle Proper Dih. Ryckaert-Bell. Improper Dih. 3.65061e+04 5.60824e+03 1.42205e+04 1.80483e+04 3.37686e+03 LJ-14 Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) 1.09448e+04 6.89125e+04 8.18947e+04 -6.41177e+03 -1.21650e+06 Coul. recip. Dis. Rest. D.R.Viol. (nm) Potential Kinetic En. -3.85131e+05 0.00000e+00 4.54606e+05 -1.36853e+06 2.44457e+05 Total Energy Temperature Pres. DC (bar) Pressure (bar) Constr. rmsd -1.12408e+06 3.10953e+02 -1.57129e+02 5.40099e+02 1.15690e-05 Step Time Lambda 29500 59.00000 0.00000 Energies (kJ/mol) Angle G96Angle Proper Dih. Ryckaert-Bell. Improper Dih. 3.66857e+04 5.65841e+03 1.39441e+04 1.81639e+04 3.44242e+03 LJ-14 Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) 1.11234e+04 6.94373e+04 8.36399e+04 -6.42711e+03 -1.21988e+06 Coul. recip. Dis. Rest. D.R.Viol. (nm) Potential Kinetic En. -3.85140e+05 0.00000e+00 4.73981e+05 -1.36935e+06 2.43700e+05 Total Energy Temperature Pres. DC (bar) Pressure (bar) Constr. rmsd -1.12565e+06 3.09991e+02 -1.57883e+02 3.05347e+02 1.18083e-05 ------------------------------------------------------- Program mpich_exe.10603, VERSION 4.5.5 Source code file: ns.c, line: 2549 Fatal error: One of the box vectors has become shorter than twice the cut-off length or box_yy-|box_zy| or box_zz has become smaller than the cut-off. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors The starting system has these dimensions 10.41535 10.32882 11.24541. Using g_energy to check the box size fluctuations, I got the following: 21 Last energy frame read 297 time 59.400 Statistics over 27501 steps [ 0.0000 through 55.0000 ps ], 1 data sets All statistics are over 2751 points Energy Average Err.Est. RMSD Tot-Drift ------------------------------------------------------------------------------- Box-X 14.3931 1.2 2.47974 8.21254 (nm) 22 Last energy frame read 297 time 59.400 Statistics over 27501 steps [ 0.0000 through 55.0000 ps ], 1 data sets All statistics are over 2751 points Energy Average Err.Est. RMSD Tot-Drift ------------------------------------------------------------------------------- Box-Y 14.2735 1.2 2.45914 8.14431 (nm) 23 Last energy frame read 297 time 59.400 Statistics over 27501 steps [ 0.0000 through 55.0000 ps ], 1 data sets All statistics are over 2751 points Energy Average Err.Est. RMSD Tot-Drift ------------------------------------------------------------------------------- Box-Z 6.63204 1 2.01081 -6.84929 (nm) The graphs of box sizes show that x and y were increasing while z was decreasing drastically before the system blew up. Apologies for such a long post. I hope someone would have some clue as to why distance restraint can't be applied to my system. Your help is much appreciated. Best wishes, Huiwen << This message and any attachment are intended solely for the addressee and may contain confidential information. If you have received this message in error, please send it back to me, and immediately delete it. Please do not use, copy or disclose the information contained in this message or in any attachment. Any views or opinions expressed by the author of this email do not necessarily reflect the views of the University of Nottingham. This message has been checked for viruses but the contents of an attachment may still contain software viruses which could damage your computer system: you are advised to perform your own checks. Email communications with the University of Nottingham may be monitored as permitted by UK & Malaysia legislation. >>
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